title: BC08_NORMAL1

extract_protocol:
InDrop v2
CD45+ cells from breast were isolated by mincing the freshly obtained surgical specimens into 1 mm cubic pieces and subsequent enzymatic digestion using LiberaseTL (Sigma) for 20 min at 37°C. The digested tissues were then passed through a 100M filter  and washed twice with PBS prior to surface staining. Immune cells were stained at 1x10^6 cells per ml for 20 min with anti-CD45 and DAPI for live-dead discrimination following Fc receptor blockade (BioLegend). Viable immune cells (CD45+DAPI-) were sorted on a FACSARIA sorter (BD Biosciences).
Sequencing libraries were prepared following the InDrop v2 protocol (see Zilinonis et al. 2017, Nature Protocols)

value: breast


title: BC07_TUMOR2

status: Public on Jun 28 2018

type: SRA

city: New York

first: Ambrose

middle: J

last: Carr

state: NY

address: 417 E 68th St

department: Computational and Systems Biology Program, SKI

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: transcriptomic

data_processing:
InDrop v2 RNA-seq data was processed from raw fastq files to count matrices with SEQC v0.2.1 (see https://github.com/ambrosejcarr/seqc.git)
Genome_build: Gencode GRCh38
Supplementary_files_format_and_content: Cell x gene unnormalized count matrices in gzipped csv format

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
InDrop v2
CD45+ cells from tumor were isolated by mincing the freshly obtained surgical specimens into 1 mm cubic pieces and subsequent enzymatic digestion using LiberaseTL (Sigma) for 20 min at 37°C. The digested tissues were then passed through a 100M filter  and washed twice with PBS prior to surface staining. Immune cells were stained at 1x10^6 cells per ml for 20 min with anti-CD45 and DAPI for live-dead discrimination following Fc receptor blockade (BioLegend). Viable immune cells (CD45+DAPI-) were sorted on a FACSARIA sorter (BD Biosciences).
Sequencing libraries were prepared following the InDrop v2 protocol (see Zilinonis et al. 2017, Nature Protocols)

tag: cell type

value: CD45+ leukocytes

tag: donor age (years)

tag: resident tissue

value: breast tumor


title: MT1.CompleteMedium.WT1.Rep1

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

country: United Kingdom

institute: University of Glasgow

data_processing:
Basecalls performed in phred64
Sequenced reads were mapped to hg19 whole genome using Tophat2 with default settings
FPKM matrix was derived using Cufflinks suite using default settings
Differential expression quantified using CuffDiff with default settings (FDR <= 0.05)
Genome_build: hg19
Supplementary_files_format_and_content: Summary files describe the results of CuffDiff differential expression analysis for core comparisons as well as FPKM matrix for all replicates created using Cufflinks suite.

molecule: total RNA

growth_protocol: Total RNA was isolated from HCT116 cells after 48 hours of glutamine starvation (GD) (Cetinbas et al., 2016) or complete medium (CM)

extract_protocol:
Qiagen RNA extraction kit. (74104, Quigen)
PolyA, paired end sequencing on Illumina NextSeq500 at the Beatson Institute of Cancer Research, UK

tag: cell line

tag: tissue

value: human colon cancer cell line

tag: growth medium

value: Grown in complete medium


title: BC07_TUMOR4


title: MT2.CompleteMedium.WT1.Rep2


title: BC10_TUMOR1

data_processing:
10x Data was processed with the Cell Ranger pipeline, version 2.1.1
Genome_build: Gencode GRCh38
Supplementary_files_format_and_content: Cell x gene unnormalized count matrices

source_name: CD3+ leukocytes

extract_protocol:
Chromium Single Cell 5′ Library & Gel Bead Kit
CD3+ cells from tumor were isolated by mincing the freshly obtained surgical specimens into 1 mm cubic pieces and subsequent enzymatic digestion using LiberaseTL (Sigma) for 20 min at 37°C. The digested tissues were then passed through a 100M filter and washed twice with PBS prior to surface staining. Immune cells were stained at 1x10^6 cells per ml for 20 min with anti-CD45 and DAPI for live-dead discrimination following Fc receptor blockade (BioLegend). Viable immune cells (CD45+DAPI-) were sorted on a FACSARIA sorter (BD Biosciences).

tag: donor

value: CD3+ leukocytes


title: BC11_TUMOR2


title: BC09_TUMOR2


title: BC05_TUMOR4


title: BC11_TUMOR1


title: BC06_TUMOR3


title: BC05_TUMOR3


title: BC05_TUMOR1


title: BC06_TUMOR2


title: BC04_BLOOD7

extract_protocol:
InDrop v2
CD45+ cells from blood were stained at 1x10^6 cells per ml for 20 min with anti-CD45 and DAPI for live-dead discrimination following Fc receptor blockade (BioLegend). Viable immune cells (CD45+DAPI-) were sorted on a FACSARIA sorter (BD Biosciences).
Sequencing libraries were prepared following the InDrop v2 protocol (see Zilinonis et al. 2017, Nature Protocols)

value: blood


title: BC04_BLOOD6


title: BC04_TUMOR6


title: BC04_TUMOR4


title: BC06_TUMOR1


title: BC04_BLOOD5


title: MT3.CompleteMedium.WT1.Rep3


title: BC09_TUMOR1


title: BC05_TUMOR2


title: BC04_TUMOR2


title: BC04_TUMOR3


title: BC04_TUMOR5


title: BC04_BLOOD3


title: BC04_BLOOD1


title: BC04_TUMOR1


title: BC04_BLOOD4


title: BC02_TUMOR4


title: BC02_NORMAL3


title: BC02_NORMAL2


title: BC02_LYMPHNODE6

extract_protocol:
InDrop v2
CD45+ cells from lymph node were isolated by mincing the freshly obtained surgical specimens into 1 mm cubic pieces and subsequent enzymatic digestion using LiberaseTL (Sigma) for 20 min at 37°C. The digested tissues were then passed through a 100M filter  and washed twice with PBS prior to surface staining. Immune cells were stained at 1x10^6 cells per ml for 20 min with anti-CD45 and DAPI for live-dead discrimination following Fc receptor blockade (BioLegend). Viable immune cells (CD45+DAPI-) were sorted on a FACSARIA sorter (BD Biosciences).
Sequencing libraries were prepared following the InDrop v2 protocol (see Zilinonis et al. 2017, Nature Protocols)

value: lymph node


title: BC04_BLOOD2


title: BC02_TUMOR2


title: BC02_LYMPHNODE4


title: BC02_TUMOR1


title: BC01_TUMOR4


title: BC02_TUMOR3


title: BC02_LYMPHNODE5


title: BC02_LYMPHNODE1


title: BC02_LYMPHNODE3


title: BC01_NORMAL4


title: BC01_NORMAL3


title: BC01_TUMOR1


title: BC01_TUMOR2


title: BC02_LYMPHNODE2


title: BC01_TUMOR3


title: Control [5061]

city: Manhattan

first: Tenzin

middle: C

last: Lhakhang

address: 550 First Avenue

institute: NYU School of Medicine

data_processing:
Tophat2 aligner against mm10 reference
Gene counting against mm10 reference utilizing htseq-count 0.8.0
Normalization of raw counts and DE test utilizing DESeq2/3.5
Genome_build: mm10
Supplementary_files_format_and_content: Normalized.counts

organism: Mus musculus

source_name: Heart Tissue

extract_protocol:
400 ng of Total RNA
Illumina Truseq Stranded Total RNA ribozero gold library prep

tag: strain

value: Cd36 loxp mice crossed Cd36 loxp mice

value: Heart Tissue


title: EC cd36 KO [5086]

source_name: Endothelial Cell cd36 KO Heart Tissue

value: Endothelial Cell cd36 KO Heart Tissue


title: Total cd36 ko [5213]

source_name: Total cd36 KO Heart Tissue

value: Total cd36 KO Heart Tissue


title: MHC cd36 KO [4920]

source_name: Cardiomyocyte cd36 KO Heart Tissue

value: Cardiomyocyte cd36 KO Heart Tissue


title: Total cd36 ko [5222]


title: MHC cd36 KO [4923]


title: Total cd36 ko [5214]


title: Control [5059]


title: EC cd36 KO [5049]


title: BC01_NORMAL1


title: BC01_NORMAL2


title: BC01_BLOOD3


title: EC cd36 KO [5051]


title: MHC cd36 KO [4922]


title: BC01_BLOOD1


title: BC11_TUMOR2_TCR

description: Contains RNA sequencing of the T-cell receptor of individual cells

extract_protocol:
Chromium Single Cell V(D)J Enrichment Kit, Human T Cell
CD3+ cells from tumor were isolated by mincing the freshly obtained surgical specimens into 1 mm cubic pieces and subsequent enzymatic digestion using LiberaseTL (Sigma) for 20 min at 37°C. The digested tissues were then passed through a 100M filter and washed twice with PBS prior to surface staining. Immune cells were stained at 1x10^6 cells per ml for 20 min with anti-CD45 and DAPI for live-dead discrimination following Fc receptor blockade (BioLegend). Viable immune cells (CD45+DAPI-) were sorted on a FACSARIA sorter (BD Biosciences).


title: CD4 T cell wildtype rep2

first: Yuheng

last: Lu

address: 417 East 68th Street

data_processing:
We preprocessed the paired-end reads using cutadapt to remove the adaptors and low-quality bases.
The processed reads were then aligned to the mouse genome (mm9) using the STAR aligner.
To account for the variation in 3’UTR usage, we only counted the reads aligned to CDS for coding genes.
The read counts per gene were further normalized as fragments per kilobase per million (FPKM) to represent the mRNA abundance.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including gene-wise CDS read counts for each sample

source_name: CD4 T cell

extract_protocol:
Total RNA was extracted from sorted cells using TRIzol LS Reagent (Invitrogen).
RNA libraries were prepared using TruSeq RNA Library Preparation Kit (Illumina).
About 25 millions of paired-end reads with 50-nucleotide length were generated for each sample and sequenced on Illumina Hi-Seq 2500 system (MSKCC iGO core facility).

tag: genotype

value: wild type

value: CD4 T cell


title: CD4 T cell wildtype rep3


title: BC11_TUMOR1_TCR


title: CD4 T cell wildtype rep1


title: BC09_TUMOR2_TCR


title: CD4 T cell miR155 KO rep3

value: miR-155 KO


title: BC10_TUMOR1_TCR


title: CD4 T cell miR155 KO rep2


title: CD4 T cell miR155 KO rep1


title: Macrophage wildtype rep3

source_name: Macrophage

value: Macrophage


title: WT.oxoG.rep3

city: Zurich

first: Shana

middle: J.

last: Sturla

address: Schmelzbergstrasse 9

department: Department of Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

library_source: genomic

data_processing:
Library strategy: click-code-seq
Raw reads were aligned to the S. cerevisiae genome (S288C) with Bowtie 2 (version 2.3.0) with --end-to-end and --trim5 8 modes
The produced SAM files were sorted and converted to BAM files with Sambamba (version 0.6.6)
PCR duplicates in BAM files were removed with samtools (version 1.3) using markdup command.
The bam files were converted to bed files directly with bedtools (version 2.25)
Based on the strand tag (+/-), 8-oxoG sites were calculated using the following rules: for read with ‘+’ tag, the 8-oxoG was located at the start site of this read; for reads with ‘–’ tag, the 8-oxoG was located at the end site of this read. The bed files with single resolution data were generated with the above rules, and used for further analysis.
Genome_build: R64
Supplementary_files_format_and_content: bedgraph files include 8-oxoG sites, the values in the fourth column present the reads number.

molecule: genomic DNA

organism: Saccharomyces cerevisiae BY4741

source_name: BY4741 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)

growth_protocol: Cells were grown in YPD overnight and harvest in early log-phase growth (OD600 = 0.5 - 1.0).

extract_protocol:
Genomic DNA from S. cerevisiae cells was grown overnight in liquid rich medium containing yeast extract, peptone and dextrose (YPD) , then extracted with a DNA Isolation Kit for Cells and Tissues (Roche Holding AG) according to the manufacturer’s instructions. To minimize adventitious 8-oxoG formation, antioxidants (100 mM deferoxamine, 100 mM butylated hydroxytoluene) were used until the 8-oxoG excision step. Genomic  DNA (5 μg) was sheared in 130 μl Tris-EDTA buffer with a Covaris S220 ultrasonicator (Covaris Inc.)
The DNA fragments were treated with APE 1 (final concentration (fc): 0.2U/μl) in 1 × NEBuffer 2.1 at 37 °C for 1 h to remove abasic sites. Dideoxynucleotides (Jena Bioscience GmbH, fc: 200 μM) and therminator IX (NEB, fc: 0.03 U/μl) were added and heated (60 °C, 10 min) to block gaps and terminal nucleotides in DNA fragments. The product was purified using the Monarch nucleic acid purification kit (NEB). The removal of 8-oxoG was carried out with 1 μl Fpg (NEB, 8 U/ μl) and 1 μl APE 1 (NEB, 10 U/μl) in 50 μl 1 × NEBuffer 2.1 at 37 °C for 1 h. The reaction mixture was then heated (60 °C, 10 min) to inactive Fpg and APE1. After allowing to return to room temperature, 1 μl of prop-dGTP (10 mM) and 0.2 μl of therminator IX (NEB, 10 U/ μl) was added and the mixture was heated (60°C, 10 min).The resulting DNA was purified with nucleic acid purification kit, completely dried on a vacuum concentrator and re-suspended in 4 μl water. Next, 6 μl L19-azido (200 μM), 2 μl potassium phosphate buffer (1 M, pH 7.0), 2 μl aminoguanidine hydrochloride solution (50 mM), 2 μl DMSO, 2 μl sodium ascorbate (25 mM) and 2 μl premixed CuSO4:THPTA (1:6, 5 mM in concentration of Cu2+) were add and incubated at room temperature (30 min). After purification, DNA (50 μl in TE buffer) was heated ( 95 °C,  2 min) and the tube was quickly transfered to an ice bath. DNA was subjected to slow rotation with Dynabeads MyOne C1 (Invitrogen Corp.) in bead-binding buffer (5 μl, 5.0 mM Tris-HCl (pH 7.5), 1.0 mM EDTA, 1 M NaCl) at room temperature. for 30 min. Afterwards, the beads were washed twice with bead-washing buffer (200 μl, 10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.2 M NaCl) and resuspended in 49 μl reaction mixture (5 μl T4 PNK reaction buffer (10 ×), 5 μl ATP (10 mM) and 39 μl ddH2O). After adding 1 μl T4 PNK (NEB), the mixture was warmed at 37 °C for 30 min. Next, the beads were washed two times with 200 μl bead-washing buffer and resuspended in 49 μl reaction mixture (5 μl T4 ligase reaction buffer (10 ×), 5 μl PEG-4000 (50 %), 0.5 μl TWEEN-20 (1 %), 3 μl pre-annealed dsDNA adapter (40 μM) ). After adding 1 μl T4 ligase (NEB), the mixture was incubated at 16 °C for 2 h. After adaptor ligation, the beads were washed twice with 200 μl bead-washing buffer, resuspended in 20 μl ddH2O and heated at 95 °C for 2 min. The beads were pelleted immediately using a magnetic rack, and the supernatant, which contained the single-stranded library molecules, was transferred to a fresh tube. The entire library was used for indexing with one of the barcoded primers, P7-index1-3, and Ex-P5 using Vent exo- polymerase (NEB) in 1 × Thermopol buffer. The indexed library was purified using an SPRIselect kit (Beckman Coulter) according to the manufacturer’s instructions. After indexing, the library was amplified with Pr-P5-2nd and Pr-P7-2nd using Q5 high fidelity DNA polymerase (NEB) and purified with an SPRIselect kit. The library size was verified using the Agilent 2200 tapestation with high sensitivity D1000 screen tape before being loaded onto the Illumina Miseq platform (Illumina).


title: BC09_TUMOR1_TCR


title: Macrophage wildtype rep1


title: Macrophage wildtype rep2


title: Macrophage miR155 KO rep3


title: WT.oxoG.rep2


title: Macrophage miR155 KO rep2


title: BC02_NORMAL1

value: breast


title: Macrophage miR155 KO rep1


title: Dendritic cell wildtype rep3

source_name: Dendritic cell

value: Dendritic cell


title: WT.oxoG.rep1


title: Dendritic cell miR155 KO rep2


title: Dendritic cell wildtype rep1


title: Dendritic cell miR155 KO rep3


title: Hepatic stellate cells lpsc1

type: RNA

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: iPSC harvested from the differentiation plate on day 0 Hepatic stellate cells lpsc1

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v3) in R.3.2.1

label: biotin

source_name: Hepatic stellate cells

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA from sorted cells was obtained using the RNeasy Micro Kit (Qiagen). Total RNA was retro-transcribed using a high capacity complementary DNA reverse-transcription kit (Applied Biosystems, Foster City, CA).


title: Fibroblast: BJ3

description: parental BJ1 fibroblast  Fibroblast: BJ3

source_name: Fibroblast (BJ1)

value: parental BJ1 fibroblast


title: Fibroblast: BJ2

description: parental BJ1 fibroblast  Fibroblast: BJ2


title: B cell wildtype rep2

source_name: B cell

value: B cell


title: B cell wildtype rep1


title: Hepatic stellate cells lhsc3p1

description: iPS-HSC cells at passage 1 Hepatic stellate cells lhsc3p1

value: iPS-HSC cells at passage 1


title: B cell wildtype rep3


title: Hepatic stellate cells DITO22

description: iPS-HSC cells at passage 1 Hepatic stellate cells DITO22


title: Hepatic stellate cells lpsc2

description: iPSC harvested from the differentiation plate on day 0 Hepatic stellate cells lpsc2


title: Hepatic stellate cells HD29

description: iPS-HSC cells at passage 1 Hepatic stellate cells HD29


title: Dendritic cell miR155 KO rep1


title: Fibroblast: BJ1

description: parental BJ1 fibroblast  Fibroblast: BJ1


title: Hepatic stellate cells lpsc3

description: iPSC harvested from the differentiation plate on day 0 Hepatic stellate cells lpsc3


title: Hepatic stellate cells iHSC_3

description: freshly isolated iPS-HSC cells (iHSC) Hepatic stellate cells iHSC_3

value: freshly isolated iPS-HSC cells (iHSC)


title: B cell miR155 KO rep3


title: B cell miR155 KO rep2


title: Dendritic cell wildtype rep2


title: B cell miR155 KO rep1


title: Hepatic stellate cells iHSC_2

description: freshly isolated iPS-HSC cells (iHSC) Hepatic stellate cells iHSC_2


title: Hepatic stellate cells iHSC_1

description: freshly isolated iPS-HSC cells (iHSC) Hepatic stellate cells iHSC_1


title: A4

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Gene expression in the adenocarcinomic human alveolar basal epithelial cells from a 58y old caucasian male.

hyb_protocol: 825 ng from each of the Cy3-labeled sample of A549 cells infected with pMIRNA1 empty vector and Cy5-labeled samples for another study were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) human (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing: The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 11.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., doi: 10.18632/oncotarget.23417.

source_name: A549 cells purchased from the American Type Culture Collection (ATCC)

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Cells were cultured following the recommendations in the Product Information Sheet (ATCC)

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: A549 cells were infected with pMIRNA1—Empty Vectors obtained from System Biosciences.

tag: infection

value: pMIRNA1 empty vector

tag: replicate

tag: Sex

value: male

tag: age

value: 58 years old

tag: race

value: caucasian

tag: status

value: lung


title: Wild Type 2mm inflorescences rep2

city: Shanghai

first: yun

last: hu

state: Shanghai

address: 800 Dongchuan Road

department: Plant Biology

country: China

institute: SJTU

description: Microarray data of genome-wide gene expression profile

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 7G.

data_processing: The data were analyzed with PARTEK genomic suit 6.4 using RMA normalization

label: boitin

organism: Oryza sativa

source_name: inflorescences in length of 2mm

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (3_ivt_express_kit_manual Affymetrix).

growth_protocol: Rice plants grow in the paddyfield

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

treatment_protocol: No special treatment

tag: genotype/variation

value: Wild Type

tag: tissues

value: inflorescences


title: osmads32 2mm inflorescences rep3

value: osmads32 mutant


title: Mouse whole kidney Vhl knockout 3 months old-2

city: Taichung

first: Tien

last: Hsu

address: No.91, Hsueh-Shih Road

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: China Medical University

hyb_protocol: Amount labeled  target hybridization to array: 15 ug

scan_protocol: Affymetrix standard protocol

data_processing:
Moderated t tests: Vhl-/- vs wild-type   Pairwise t tests were performed for each gene between Vhl genotypes. A moderated t test was used, which is a Bayesian analysis that does not test each gene independently, but rather, leverages information from all of the genes on the array to increase statistical power over a standard two-sample Student t test. It is especially helpful when sample sizes are small.   Benjamini-Hochberg False Discovery Rate (FDR) correction was then applied to obtain FDR-corrected p values ('q' values), which represent the probability that a given result is a false positive based on the distribution of all p values on the array. Corrected/adjusted p values such as the FDR q are the best measure of significance for a given test when many hypotheses (e.g., ~25,000 genes) are tested at once.
The arrays were normalized together using the Robust Multiarray Average (RMA) algorithm and a CDF (Chip Definition File) that maps the probes on the array to unique Entrez Gene identifiers. The result is a matrix in which each row corresponds to an Entrez Gene ID and each column corresponds to a sample. The expression values are log2-transformed by default. The technical quality of the arrays was assessed by two quality metrics: Relative Log Expression (RLE) and Normalized Unscaled Standard Error (NUSE). For each sample, median RLE values > 0.1 or NUSE values > 1.05 are considered out of the usual limits, although RLE is the quality metric most strongly associated with technical quality. All arrays had median RLE and NUSE values well within these limits.

label_protocol: Affymetrix standard protocol

growth_protocol: Mice were grown to 3 months when whole kidneys were resected

extract_protocol: Resected kidneys were frozen in liquid nitrogen, minced in tissue grinder, and total RNA purified using Trizol and Qiagen RNeasy

treatment_protocol: No additional treatment

tag: gender

value: Male

value: kidney

value: Floxed Vhl allele with Hoxb7-Cre-GFP


title: Wild Type 2mm inflorescences rep1


title: A2

value: adenocarcinomic human alveolar basal epithelial cells


title: Wild Type 2mm inflorescences rep3


title: Mouse whole kidney wild-type 3 months old-1

value: Floxed Vhl allele


title: A3


title: osmads32 2mm inflorescences rep1


title: Mouse whole kidney wild-type 3 months old-2


title: Mouse whole kidney wild-type 3 months old-3


title: Mouse whole kidney Vhl knockout 3 months old-3


title: A1


title: HCC2.4

city: Paris Cedex 15

first: Oliver

last: Bischof

address: 28 rue du Docteur Roux

department: Cell Biology & Infection

country: France

institute: Institut Pasteur

hyb_protocol: Subsequent hybridization, wash, and staining were carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit and the manufacturer's protocols were followed. Briefly, each fragmented and labeled single-strand cDNA target sample (approximately 3.5 µg) was individually hybridized to a GeneChip Mouse Gene 2.0 ST Array at 45°C for 16 h in Affymetrix GeneChip Hybridization Oven 640.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 scanner.

data_processing:
Raw Affymetrix Mouse Gene 2.0 ST array intensity data were analyzed using open-source Bioconductor packages on R. The data were normalized all together (4 HCC and 4 ICC) using the robust multi-array average normalization approach implemented in the oligo package67. Internal control probe sets were removed and average expression deciles over conditions were then defined. Probes whose average expression was lower than the 4th expression decile were removed for subsequent analyses. To remove sources of unwanted variation and consider potential batch effects, data were finally corrected with the sva package. To get as much information as possible, we combined Affymetrix Mouse Gene 2.0 ST annotations provided by Affymetrix and Ensembl through the packages pd.mogene.2.0.st and biomaRt68. Principal component analysis and bi-clustering based on Pearson’s correlation and Ward’s aggregation criterion were used to check for consistency between biological replicates and experimental conditions at each step of the pre-processing.
Normalized log-scaled and filtered expression data were further considered for differential analysis with limma69. Briefly, a nested general linear model considering tumour type (HCC or ICC), gender (male or female) and their interaction was fitted to the data. Moderated F-statistics that combines the empirical Bayes moderated t-statistics for all contrasts into an overall test of significance for each probe were used to assess the significance of the observed expression changes when comparing HCC and ICC. p-values were corrected for multiple testing using the FDR approach for a significance level of 0.1. A cut-off in fold-change at 1.5 was finally applied.

source_name: Hepatocellular carcinoma

label_protocol: Fragmented and labeled DNA targets were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol from 100 ng total RNA starting material and 5.5 µg single strand cDNA.

growth_protocol: Cells were grown in DMEM with 10% FCS in 7.5% CO2

extract_protocol: RNA was extracted using the QIAGEN RNAeasy Plus kit according to the manufacturer's instructions.

treatment_protocol: no treatment has been performed

value: female

tag: cell line source tumor type

value: Hepatocellular carcinoma


title: THP1 Bi-cel-67 - Input [THP12012 cel_i]

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

description: THP12012 cel_i raw

hyb_protocol: according to manufacturers (Affymetrix) instructions

data_processing: For HEK293 and THP1 pulldowns, gene expression was obtained using the RMA algorithm output from the GCOS Affymetrix software with a raw value cut-off of 5 in pulldown samples. The inputs and pulldown samples were normalized separately to show change relative to the Bi-cel-67 control. Results visualized in GeneSpring and AltAnalyze version 2.0.9 (http://altanalyze.org/) for any Ensembl version 72 gene aligning probesets transcript clusters98-100. miR-196 targets genes are reported for independent pulldowns with a 2-fold increase in the miR-196b pulldown fractions compared to the cel-67 pulldown controls.

source_name: THP1 Bi-cel-67 control - Input

growth_protocol: HEK293T cells were cultured in DMEM (ThermoFisher Scientific) containing 10% heat-inactivated FBS (Atlanta Biologics), Pen-Strep (ThermoFisher Scientific), and L-Glutamine (ThermoFisher Scientific). THP1 cells were cultured in RPMI 1640 (ThermoFisher Scientific) containing 20% heat-inactivated FBS (Atlanta Biologics), Pen-Strep (ThermoFisher Scientific), and L-Glutamine (ThermoFisher Scientific). Cells were maintained in liquid culture at subconfluency at low passage at 37°C in 5% CO2.

extract_protocol: 10% of cytosolic lysates were mixed with TriZol LS (Ambion) as “Input” control, while the remaining lysates were subjected to “Pulldown” by mixing with M-280 Dynabeads (Invitrogen) for four hours rotating at 4°C. Dynabeads were prepared in advance for RNA use according to manufacturers instructions, then rinsed in cold lysis buffer and blocked with rotation at 4°C for 2 hours with Yeast tRNA (Invitrogen) and BSA (Invitrogen). After the pulldown incubation, beads were washed on a magnetic stand 3 times with ice cold wash buffer (Nonne et al., 2010) for 3 minutes rotating at 4°C. After the last wash beads were resuspended in 0.75ml TriZol LS and brought to 1ml with nuclease free water (ThermoFisher Scientific) then frozen at -80°C. RNA was extracted using TriZol or TriZol LS (Ambion) as previously described (Meyer et al., 2009). miR mimic pulldown and input control RNA samples analyzed on an Agilent Bioanalyzer with a RIN >8.0 were selected for microarray processing. 550-1000pg of matched input and pulldown RNA samples from three independent THP1 experiments were processed using the Ovation Pico WTA System V.2 (Nugen) and hybridized to Human 1.0ST arrays (Affymetrix). 1000pg of matched input and pulldown samples from one experimental replicate of HEK293 cells was also analyzed using the same platforms.

treatment_protocol: For Bi-miR pulldowns, 0.2x106 HEK 293 cells were plated overnight then co-transfected the following day with 100nM biotinylated miRNA mimics and 0.5mg/ml GFP-Max (Lonza) with CaCl2 BBS. For Bi-miR pulldowns, 1x106 THP1 cells were co-transfected with 100nM biotinylated miR mimics and 0.5μg/ml GFP-Max by electroporation using Amaxa Nucleofector 4D and cell line SG kit (Lonza) according to manufacturer instructions. Twenty-four hours after transfection, cells were lysed on ice in a cytosolic lysis buffer RLN (Qiagen) with 1x HALT protease inhibitor tab (Roche), RNaseI (Ambion), and 1mM DTT (Sigma). Nuclei were pelleted at 10,000g for 10min at 4°C and discarded.

tag: cell type

value: acute myeloid leukemia cell line

tag: molecule subtype

value: cytosolic RNA


title: HEK293 Bi-cel-67 - Pulldown [293 cel_p]

description: 293 cel_p raw

scan_protocol: according to manufacturers (Affymetrix) instructions

source_name: HEK293 Bi-cel-67 control - Pulldown

tag: cell line

value: embryonic kidney cell line


title: shp53 16 hr TNF-a H3K4me1 ChIP-seq

city: San Diego

first: Shannon

middle: M

last: Lauberth

state: California

address: 9500 Gilman Drive #0322, Bonner Hall 3202

department: Biological Sciences

institute: UCSD

description:
Shp5316hr_H3K4me1_rep1_S6_L007_R1_001
Shp5316hr_H3K4me1_rep2_S9_L006_R1_001

data_processing:
Sequenced reads were mapped to the hg38 human reference genome using Bowtie2 software and default parameters.
Mapped reads were then processed to make tag directories using the HOMER module. PCR duplications were removed and only uniquely mapped reads were kept for further analyses.
Genome browser files for resulting reads were generated by using the makeUCSCfile module from HOMER.
Enrichment for mutant p53 and H3K4me1 deposition were called using findPeaks module from HOMER using preset parameters for transcription factors and histones, respectively and compared to the input samples.
Deeptools were used to generate heatmaps.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: SW480 Cells

growth_protocol: Human SW480 cells were grown in Dulbecco’s modified Eagle medium (DMEM, Gibco) medium supplemented with 10% FBS. SW480 cells that stably and inducibly express short hairpins against LacZ or p53 were kindly provided by Xinbin Chen (UC Davis) and were grown in standard DMEM medium containing 1X penicillin and streptomycin (Gemini Bio-Products), 1.5 μg ml-1 puromycin (Sigma), and were induced with 1 μg ml-1 doxycycline (Sigma).

extract_protocol:
For ChIP, cells were crosslinked, lysates from sonicated nuclei were prepared, and protein-DNA complexes were immunoprecipitated with corresponding antibodies. Please refer to the methods section for detailed protocols.
ChIP-seq libraries were prepared according to Illumina's ChIP Truseq protocol. Briefly, ChIP DNA was end-repaired and adaptors were ligated to the ends of the DNA fragments. Adaptor-ligated ChIP DNA fragments with average size of 350 bp were used to construct libraries and single-end sequenced on Illumina HiSeq 4000.

treatment_protocol: All cells were treated with 12.5 ng/ml TNF-a (Shenandoah Biotechnology) for 16 hr before harvesting for ChIP-seq analyses.

value: Colon Cancer Cells

value: Human Colon Cancer Cell Line, stable p53 knockdown

tag: treatment

value: TNF-a

tag: chip antibody

value: anti-H3K4me1 (ab8895)


title: shLacZ 16 hr TNF-a p53 ChIP-seq

description:
ShLacZ16hr_p53_rep1_S1_L006_R1_001
ShLacZ16hr_p53_rep2_S2_L006_R1_001

value: Human Colon Cancer Cell Line, stable control (LacZ) knockdown


title: shLacZ 16 hr TNF-a H3K4me1 ChIP-seq

description:
ShLacz16hr_H3K4me1_rep1_S5_L007_R1_001
ShLacZ16hr_H3K4me1_rep2_S8_L006_R1_001


title: osmads32 2mm inflorescences rep2

value: inflorescences


title: shp53 16 hr TNF-a p53 ChIP-seq

description:
Shp5316hr_p53_rep1_S3_L006_R1_001
Shp5316hr_p53_rep2_S4_L006_R1_001


title: HEK293 Bi-cel-67 - Input [293 cel_i]

description: 293 cel_i raw

source_name: HEK293 Bi-cel-67 control - Input

label_protocol: according to manufacturers (Affymetrix) instructions


title: HEK293 Bi-miR-196b - Input [293 196_i]

description: 293 196_i raw

source_name: HEK293 Bi-miR-196b - Input


title: THP1 Bi-miR-196b - Input [THP12012 196_i]

description: THP12012 196_i raw

source_name: THP1 Bi-miR-196b - Input


title: THP1 Bi-miR-196b - Pulldown [THP12012 196_p]

description: THP12012 196_p raw

source_name: THP1 Bi-miR-196b - Pulldown


title: HEK293 Bi-miR-196b - Pulldown [293 196_p]

description: 293 196_p raw

source_name: HEK293 Bi-miR-196b - Pulldown


title: Mouse whole kidney Vhl knockout 3 months old-1

tag: strain

tag: tissue


title: THP1 Bi-cel-67 - Pulldown [THP12012 cel_p]

description: THP12012 cel_p raw

source_name: THP1 Bi-cel-67 control - Pulldown


title: 16 hr TNF-a MLL4 ChIP-seq

description:
SW48016hr_MLL4_rep1_S8_L007_R1_001
SW48016hr_MLL4_rep2_S34_R1_001

value: control

value: anti-MLL4 provided by Kai Ge (NIH)


title: BC03_TUMOR3_4

value: CD45+ leukocytes

tag: donor age (years)

tag: resident tissue

value: breast tumor


title: BC03_TUMOR5


title: BC03_TUMOR1


title: H1-2: Stem from hight inbred lines

city: Hefei

first: Hengsheng

last: Wang

address: Changjiang Rode 130

institute: Anhui Agriculture University

data_processing:
The raw sequencing reads from all the runs were first trimmed for lo- quality regions and adapter  sequences. Reads containing N (indicating uncertain base information) greater than 10% were removed, and low quality reads were removed. Clean reads (~90% of the total read count) were mapped to the maize genome (B73_RefGen_v4 annotation build, http://plants.ensembl.org/Zea_mays/Info/Index) and a recent internal maize transcriptome using Tophat 2 with default parameters (Pertea 2010). The DESeq Bioconductor package (Version: 1.28.0) was used to normalize the mapped reads. Data quality analysis was evaluated by visualizing the results of principal component analysis (PCA).
The mapped sequence reads for all of the identified genes were used for differential expression analysis by the DESeq method. Using Cufflinks 2.2.1 and Cuffdiff, gene expression levels were calculated as reads per kilobase of transcript sequence per million base pairs sequenced (FPKM) (Trapnell et al. 2016). Based on statistical analyses, genes with a P-value < 0.05 and an absolute value |log2 ratio ≥ 1| were considered to be significant differentially expressed genes (DEGs). GO enrichment analysis was conducted using Blast2GO (https://www.blast2go.com/) with FDR < 0.05. Based on their expression patterns, the DEGs were clustered by the Genesis K-means method
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

organism: Zea mays

source_name: Stem from hight inbred lines

growth_protocol: Two different maize inbred lines, with extremely distinct plant height, which were further classified into low (L) and high (H) group. were selected for RNA sequencing at big flare period

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.  1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x100 paired end flow cell.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four samples from the low and high hybrid at big flare period were used for RNA sequencing.

tag: line

value: stem


title: HCC2.1


title: THP1 Bi-miR-196b - Pulldown [196jan14_PD]

description: 196jan14_PD raw


title: H1-1: Stem from hight inbred lines


title: HCC4

value: male


title: BC03_NORMAL4_5

extract_protocol:
InDrop v2
CD45+ cells from breast were isolated by mincing the freshly obtained surgical specimens into 1 mm cubic pieces and subsequent enzymatic digestion using LiberaseTL (Sigma) for 20 min at 37°C. The digested tissues were then passed through a 100M filter  and washed twice with PBS prior to surface staining. Immune cells were stained at 1x10^6 cells per ml for 20 min with anti-CD45 and DAPI for live-dead discrimination following Fc receptor blockade (BioLegend). Viable immune cells (CD45+DAPI-) were sorted on a FACSARIA sorter (BD Biosciences).
Sequencing libraries were prepared following the InDrop v2 protocol (see Zilinonis et al. 2017, Nature Protocols)

value: breast


title: L1-1: Stem from low inbred lines

source_name: Stem from low inbred lines

value: Chuan 29


title: L1-2: Stem from low inbred lines


title: THP1 Bi-miR-196b - Pulldown [196jan3_PD]

description: 196jan3_PD raw

value: acute myeloid leukemia cell line


title: HCC1

value: Hepatocellular carcinoma


title: BC03_NORMAL2_3


title: BC03_NORMAL1


title: THP1 Bi-miR-196b - Input [196jan3_I]

description: 196jan3_I raw

value: cytosolic RNA


title: THP1 Bi-miR-196b - Input [196jan14_I]

description: 196jan14_I raw


title: ICC2.9

source_name: Intrahepatic cholangiocarcinoma

value: Intrahepatic cholangiocarcinoma


title: ICC2.7


title: THP1 Bi-cel-67 - Pulldown [cel67-ctrljan14_PD]

description: cel67-ctrljan14_PD raw


title: ICC10

value: female


title: ICC9


title: THP1 Bi-cel-67 - Pulldown [cel67-ctrljan3_PD]

description: cel67-ctrljan3_PD raw


title: THP1 Bi-cel-67 - Input [cel67-ctljan14_I]

description: cel67-ctljan14_I raw


title: Omega17_2

status: Public on Jun 27 2018

city: Bangalore

first: Deepesh

last: Nagarajan

state: Karnataka

address: FB-04, B-wing, Department of Biochemistry, New Biology Building, IISc

department: Department of Biochemistry

country: India

institute: Indian Institute of Science

description:
E.coli (P1645ec)
Gene expression after 24hr growth in LB broth (1 ug/ml, 0.5x MBC)

hyb_protocol: Agilent’s In situ Hybridzation kit 5188-5242

scan_protocol: Standard Agilent scanning protocol

data_processing: Samples were background corrected using the normexp() function in the Limma package in R. This was followed by quantile normalization and log2 transformation.

organism: Escherichia coli

source_name: bacterial pellet

label_protocol: Samples were labeled using the Agilent Quick-Amp labeling Kit. QC was performed using Nanodrop.

growth_protocol: all cultures were grown in 10 ml LB broth at 37C/180rpm for 24 hours and flash-frozen with liquid nitrogen.

extract_protocol: RNA was extracted using Qiagen’s RNeasy minikit Cat#74106

tag: media

value: LB broth


title: THP1 Bi-cel-67 - Input [cel67-ctljan3_I]

description: cel67-ctljan3_I raw


title: Control_2

description:
E.coli (P1645ec)
Gene expression after 24hr growth in LB broth (untreated)


title: Omega76_2

description:
E.coli (P1645ec)
Gene expression after 24hr growth in LB broth (2 ug/ml, 0.5x MBC)


title: NN2_0018_1

description:
E.coli (P1645ec)
Gene expression after 24hr growth in LB broth (4 ug/ml, 0.5x MBC)


title: Control_1


title: Omega76_1


title: NN2_0018_2


title: Omega17_1


title: Frozen tissue, SMT, replicate 1

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

institute: CIPF

description:
SMT1
SMT, replicate 1, serrated
SAC (serrated, adenomacarcinoma)

hyb_protocol: A 2000ng cRNA product was hybridized with Whole Human Genome Oligo Microarray Kit (Agilent p/n G2519F-014850) containing 41,000+ unique human genes and transcripts.

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA) according to the manufacturer’s protocol.

data_processing:
Data extracted using Agilent Feature Extraction Software 10.7.1 following the Agilent grid template 014850_D_F_20100430 protocol GE1_107_Sep09 and the QC Metric Set GE1_QCMT_Sep09.
Agilent raw data were pre-processed using Agilent background correction, and quantile normalization was applied to obtain homogeneous scales in all samples.

source_name: SMT

label_protocol: Total RNA was quantified by spectrometry (NanoDrop ND1000, NanoDrop Technologies, Wilminton, Delaware USA) and fragment size distribution was analysed by RNA 6000 Pico Bioanalyzer assay (Agilent Technologies, Palo Alto, California USA). RNA 150ng was concentrated in a SpeedVac to a working dilution and used to produce Cyanine 3-CTP-labeled cRNA using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305) according to the ‘One-Color Microarray-Based Gene Expression Analysis’ protocol Version 6.0 (Agilent p/n G4140-90040). This method uses T7 RNA polymerase which simultaneously amplifies target material and incorporates cyanine 3- labelled CTP.

growth_protocol: The clinico-pathological features of the patients have been previously reported. Updated follow-up information was obtained from cancer registry files and approval for the study was granted by the Local Ethical Board. SACs were diagnosed on the basis of criteria proposed by Mäkinen et al., and hMSI-Hs according to prior established criteria (mucinous, signet-ring cell, and medullary carcinoma, tumor infiltrating and peritumoral lymphocytes, “Crohn-like” inflammatory response, poor differentiation, tumor heterogeneity, and “pushing” tumor border).

extract_protocol: A volume of approximately 10mm3 was extracted from each frozen tissue using the disposable sterile biopsy punch Acupunch 2mm (Acuderm Inc, Lauderdale, FL, USA). RNA was extracted following the manufacturer´s instructions (Qiagen, Hilden, Germany). Briefly, tissue was disrupted and homogenized in 700µl of Qiazol (Qiagen ref:1023537) using a Tissueruptor by Qiagen for 20 seconds. The homogenate was incubated at room temperature for 5 minutes. After adding 140µl of chloroform and centrifuging at 12,000xg for 15 minutes at 4ºC, 350µl of the aqueous phase was subjected to automatic total RNA extraction using the Qiacube equipment and the miRNeasy Mini Kit (ref:217004), both provided by Qiagen.

treatment_protocol: Frozen samples of 11 SACs and four hMSI-H were retrieved from the Santa Lucia University Hospital, Cartagena, Spain and used for the gene expression microarray study.

value: colorectal carcinoma

tag: crc type

value: serrated

tag: crc subtype

value: SMT (serrated, mucinous, tumour tissue)


title: Frozen tissue, SMT, replicate 3

description:
SMT3
SMT, replicate 3, serrated
SAC (serrated, adenomacarcinoma)


title: Frozen tissue, ST, replicate 5

description:
ST5
ST, replicate 5, serrated
SAC (serrated, adenomacarcinoma)

source_name: ST

value: ST (serrated, tumor tissue)


title: Kidney Control_199

city: Irvine

first: Shlomit

last: Radom-Aizik

state: CA

address: 101 Academy

department: Pediatrics

institute: University of California, Irvine

hyb_protocol: Ten μg of fragmented target cRNA was hybridized on an Affymetrix GeneChip® Porcine Genome Array.

scan_protocol: Arrays were scanned using GeneChip® Scanner 3000 7G and Command Console Software v 3.2.3. was used to produce CEL files.

data_processing: The results were analyzed using GeneSpring GX 12.1 Software (Agilent Technologies, Inc.).

organism: Sus scrofa

source_name: Porcine kidney control

label_protocol: First-strand cDNA was synthesized from 250 ng of isolated total RNA for each samples. After making the complementary second strand, the double-stranded cDNA is used to generate biotin-tagged cRNA from an in- vitro transcription (IVT) using T7 RNA polymerase.

extract_protocol: Total RNA was extracted from the porcine kidney tissue using TRIzol®

treatment_protocol: Twenty porcine were randomized into two groups:  a control group (burr hole, catheters, and anesthesia only) and a ND group (control intervention plus inflation of subdural balloon catheter and confirmation of ND).  Animals were supported on mechanical ventilation for six hours after randomization and 2 cc/kg boluses of 0.9% NaCl were given as needed to maintain a mean arterial pressure above 35 mmHg.  A laparotomy was then performed and two kidney specimens were obtained and snap frozen.

value: Porcine kidney


title: LowMg LFD 4: Low magnesium low fat diet

city: Nijmegen

first: Steef

last: Kurstjens

address: Geert Grooteplein Zuid 30

department: Physiology

country: Netherlands

institute: Radboudumc

data_processing:
Performed by BGI - China
Clean reads were mapped to Mus musculus transcriptome (GRCm38/mm10) using the HISAT/Bowtie2 tool (RRID:SCR_005476). RSEM software v1.2.31 (RRID:SCR_013027) was used to quantify gene expression levels (fragments per kilobase million (FPKM) values). FPKM values were log2 transformed and further analysed in R (www.r-project.org, v3.4.1., RRID:SCR_001905). Heatmaps for individual GO terms were created using the ggplot2 library (r-project)

source_name: epidydymal white adipose tissue

extract_protocol:
epididymal white adipose tissue was removed and snap-frozen in liquid nitrogen. Total RNA was isolated using TRIzol and treated with DNAse
Performed by BGI - China

value: epidydymal white adipose

tag: 17-week diet

value: Low magnesium low fat diet (LowMg LFD)


title: LowMg LFD 3: Low magnesium low fat diet


title: LowMg LFD 5: Low magnesium low fat diet


title: Frozen tissue, SPT, replicate 1

description:
SPT1
SPT, replicate 1, serrated
SAC (serrated, adenomacarcinoma)

source_name: SPT

value: SPT (serrated, poorly differentiated, tumour tissue)


title: Frozen tissue, MSI-H, replicate 3

description:
MSI3
MSI-H, replicate 3

source_name: MSI-H

value: microsatellite instability

value: MSI-H


title: Frozen tissue, SMT, replicate 2

description:
SMT2
SMT, replicate 2, serrated
SAC (serrated, adenomacarcinoma)


title: Frozen tissue, SMT, replicate 4

description:
SMT4
SMT, replicate 4, serrated
SAC (serrated, adenomacarcinoma)


title: Frozen tissue, MSI-H, replicate 2

description:
MSI2
MSI-H, replicate 2


title: Frozen tissue, ST, replicate 1

description:
ST1
ST, replicate 1, serrated
SAC (serrated, adenomacarcinoma)


title: Frozen tissue, ST, replicate 4

description:
ST4
ST, replicate 4, serrated
SAC (serrated, adenomacarcinoma)


title: Frozen tissue, MSI-H, replicate 4

description:
MSI4
MSI-H, replicate 4


title: Kidney Control_197


title: Frozen tissue, ST, replicate 3

description:
ST3
ST, replicate 3, serrated
SAC (serrated, adenomacarcinoma)


title: Frozen tissue, ST, replicate 6

description:
ST6
ST, replicate 6, serrated
SAC (serrated, adenomacarcinoma)


title: Frozen tissue, MSI-H, replicate 1

description:
MSI1
MSI-H, replicate 1


title: LowMg HFD 3: Low magnesium high fat diet

value: Low magnesium high fat diet (LowMg HFD)


title: LowMg LFD 1: Low magnesium low fat diet


title: LowMg LFD 2: Low magnesium low fat diet


title: LowMg HFD 2: Low magnesium high fat diet


title: LowMg HFD 1: Low magnesium high fat diet


title: LowMg HFD 5: Low magnesium high fat diet


title: Frozen tissue, ST, replicate 2

description:
ST2
ST, replicate 2, serrated
SAC (serrated, adenomacarcinoma)


title: Kidney Control_157


title: Kidney Control_187


title: Kidney Control_190


title: HFD 1: Normal magnesium high fat diet

value: Normal magnesium high fat diet (NormMg HFD)


title: HFD 4: Normal magnesium high fat diet


title: Kidney Control_184


title: Kidney Control_156


title: Kidney Control_02


title: LowMg HFD 4: Low magnesium high fat diet


title: Control 5: Normal magnesium low fat diet

value: Normal magnesium low fat diet (NormMg LFD)


title: Control 3: Normal magnesium low fat diet


title: HFD 2: Normal magnesium high fat diet


title: HFD 5: Normal magnesium high fat diet


title: Kidney Control_155


title: Kidney following ND_92

source_name: Porcine kidney six hours after Neurologic Death (ND)


title: Kidney following ND_194


title: Kidney Control_134


title: HFD 3: Normal magnesium high fat diet


title: Kidney following ND_193


title: Kidney following ND_86


title: Control 4: Normal magnesium low fat diet


title: Kidney following ND_198


title: Promoter Capture Hi-C preB aged 2

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

data_processing:
Libraries were sequenced on the IlluminaHiSeq1000/2500 platforms using the default RTA analysis software.
Sequencing reads were trimmed using trim galore v0.4 using default parameters to remove the standard Illumina adapter sequence. Reads were mapped to the mouse GRCm38 genome assembly using bowtie2 v2.2.5 using default parameters. BAM files imported to SeqMonk and reads were extended by 200bp at their 5’ end to approximate the true insert size.
RNA-seq: Reads were mapped using Hisat2. Seqmonk V1.39 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) was used for quality control, visualization and quantification of raw read counts. Total RNA was quantified over genes, whilst nuclear RNA was quantified using the active transcription pipeline which counts reads over intronic sequences.   MicroRNA-seq: Annotations from Ensembl and miRBase were merged and deduplicated. Reads were mapped using bowtie 2, and strand-specific raw read counts were generated using Seqmonk.  ATAC-seq: Reads were mapped with bowtie2. Peaks were called with MACS2 (--nomodel --shif -25 --extsize 50 –q 0.01) and filtered to exclude any for which the read counts with mapping quality score > 30 was less than 64, or that overlapped with a blacklisted region. For each condition (young and aged) peaks present in 3 out of 4 replicates were accepted and any peaks closer than 100bp to each other were merged. Raw read counts were generated over the union of peaks in young and aged used featureCounts (Liao et al., 2014).  ChIP-seq: Reads were mapped using bowtie2. Peaks were called using MACS2 with default parameters for narrow peaks for all datasets except H3K27me3 for which we used MACS1.4 to call broad peaks. Similar to ATAC-seq, peaks with low numbers of high quality reads or overlapping blacklisted regions were filtered out, and peaks for each condition were accepted if they were present in both replicates. Raw read counts over the union of peaks from young and aged were generated using featureCounts.  Hi-C/Promoter Capture Hi-C: Reads were mapped and filtered using HiCUP (Wingett et al., 2015),and Hi-C was then analysed using HOMER (Heinz et al., 2010). Interactions for promoter capture HiC were called using Chicago (Cairns et al., 2016).
Genome_build: GRCm38
RNA report: Genomic locations and raw read counts over genes (total RNA), or specifically counted over introns as a measure of active transcription (nuclear RNA). Assumed opposing strand specificity.
MicroRNA report: Genomic locations and raw, strand-specific read counts over microRNAs.
ATAC ChIP report: Read counts over union of MACS peaks from young and aged cells; peaks called by MACS2 except for H3K27me3 for which broad peaks were called with MACS1.4.
Hi-C report: Scores for PC1 from principle component analysis of interaction profiles for 250 kb bins genome-wide. Scores are aligned with H3K4me3 ChIP-seq data such that a positive score indicates an active A compartment, and a negative score an inactive, B compartment.
PCHi-C report: Chicago interaction scores for the union of significant interactions (threshold score >= 5) in aged and young. Genomic locations of the HindIII fragments at both ends of the interaction are provided, as well as the gene(s) overlapping the bait and other end of the interaction (for bait-to-bait interactions) and Chicago scores for young and aged.

source_name: bone marrow

growth_protocol: All cells were depleted of non-B lineage cells by magnetic cell sorting, and then flow sorted for pro-B and pre-B cells, directly from bone marrow single cell suspensions from young and aged mice

extract_protocol:
RNA-seq: For nuclear RNA-seq nuclei were isolated from 1-10 x 106 flow sorted B lymphocytes by incubation in 50 mM Tris-HCl pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 0.4% NP40 for 5 min on ice followed by centrifugation at 500 x g. Total and nuclear RNA was isolated with a RNeasy mini kit (Qiagen) and treated with Turbo DNAse (Ambion).  Total RNA was depleted of ribosomal RNA using a Ribo-Zero Gold rRNA removal kit (Human/Mouse/Rat:Illumina) according to the manufacturer’s instructions.  miRNA-seq: Short RNAs were isolated from 1-10 x 106 flow sorted B lymphocytes using a mirVANA kit (Ambion/ThermoFisher).  ATAC-seq: ATAC-seq was performed directly on 5 x 104 flow sorted B lymphocytes.  ChIP-seq: Flow sorted B lymphocytes were fixed in 1% formaldehyde for 10 min at RT, quenched with 125mM glycine, washed with PBS and pellets snap frozen for storage at -80°C. Cells were lysed (150mM NaCl/25mM Tris pH 7.4/5mM EDTA/0.1% Triton/1% SDS/protease inhibitors; + 20mM Sodium Butyrate for H3K27ac), chromatin sonicated and diluted 5-10 times (0.01% SDS/1.1% Triton/1.2mM EDTA/16.7mM Tris pH 8.1/167mM NaCl; or for H3K27ac in RIPA buffer: 10 mM Tris-HCl pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate) and incubated with antibody overnight at 4°C before addition of protA-G magnetic beads. For H3K27ac, antibody was instead pre-incubated with beads and washed with RIPA buffer before incubation with chromatin at 4°C overnight. Beads were washed once with Low Salt buffer (0.1% SDS, 0.1% SDS, 2mM EDTA, 20mM Tris pH 8.0, 150mM NaCl), twice with High Salt buffer (0.1% SDS, 0.1% SDS, 2mM EDTA, 20mM Tris pH 8.0, 500mM NaCl) and twice with TE (10mM Tris pH 8.0, 1mM EDTA). For CTCF the last High Salt buffer was substituted with LiCl Buffer (0.25M LiCl, 1% IGEPAL, 1% deoxycholic acid, 1mM EDTA, 10mM Tris, pH 8.1). For H3K27ac the first 3 washes were performed with RIPA buffer. DNA was eluted in 0.1M NaHCO3/1% SDS and reverse-crosslinked with Proteinase K (Ambion); ChIP and input DNA was purified using the QIAquick PCR Purification Kit (Qiagen).  Hi-C/Promoter Capture Hi-C: Hi-C and Promoter CHi-C libraries were generated as described (Schoenfelder et al., 2015), with modifications as described below. 3.2-3.5 x 107 pre-B cells, pooled from several FACS sorts, were used for each library. DNA digestion was performed with 1500 units HindIII (NEB) per 5 million cells. After the biotin fill-in, in-nucleus ligation was performed as described previously (Nagano et al., 2015) for four hours at 16°C (5.5 ml 50 mM Tris-HCl, 10 mM MgCl2, 1 mM ATP, 10 mM DTT, 100 µg/ml BSA + 50 units T4 DNA ligase (Life Technologies)). An additional Proteinase K incubation (65 µl of 10mg/ml) for two hours was included after the overnight incubation, preceding RNase A treatment, two sequential phenol/chloroform (Sigma) extractions and DNA precipitation including three 70% ethanol washes. Biotin removal from non-ligated fragment ends was followed by phenol/chloroform purification and DNA precipitation.
RNA-seq: Paired-end strand-specific libraries were generated as described (Parkhomchuk et al., 2009) except polyA+ RNA selection was omitted, first strand cDNA synthesis was performed with random hexamer primers, and double-stranded cDNA was fragmented with a Covaris E220 sonicator.   miRNA-seq: Libraries were generated using the NEBNext small RNA library prep set for Illumina with 15 cycles of PCR. Transfer RNA and ribosomal RNA derived fragments were removed from the libraries by ‘double-sided’ AMPure XP size selection as described in the user manual.  ATAC-seq: Atac-seq was performed as described in Buenrostro et al. (2015).  ChIP-seq: Library preparation was performed from 0.2-0.8 ng of purified DNA using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® with the following modifications: Illumina Tru-Seq adaptors were used and library amplification was performed with the KAPA PCR Amplification kit (KAPA, Cat. KK2501) using 15 cycles.   Hi-C/Promoter Capture Hi-C: Libraries were generated essentially as described in Schoenfelder et al. (2015).

value: bone marrow

tag: age of mouse (months)

value: 18-22 months

value: flow sorted pre-B cells

tag: markers

tag: hi-c restriction enzyme

value: HindIII


title: WildType_DRIP-seq_IP

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

data_processing:
Library strategy: DRIP-Seq
Read quality testing and filtering (trimming of adapters and barcodes, filtering of non-template reads, polyclonal reads, and low-quality/uncertain calls) was performed using the Torrent Suite™ software 4.4.3.
Alignment was performed to reference genome S. cerevisiae sacCer3 (64-1-1_20110203), using the TMAP algorithm (the Torrent Mapping Alignment Program for Ion torrent) present in the Torrent suit software 4.4.3.
Duplicate reads (same start and end coordinates) were removed using SAMtools v1.7.
Read count normalization and bigwig preparation was performed using scripts available from El Hage et al. (2014).
Peak identification was performed using MACS2 2.1.1.20160309 analyzing the enrichment of IP (treatment) over the input (control), assuming a Poisson distribution (bdgcmp command) to later on perform a peak call (bdgpeakcall) with parameters (cutoff: 0.05, min length: 200 bp and max. gap 150 bp).
Genome_build: sacCer3
Supplementary_files_format_and_content: Intergenic scaled bigwig files were processed adapting the procedure described at El Hage et al. (2014). LogFE scaled bigwig file was created from these scaled bw using MACS2, as well as the bed file.

organism: Saccharomyces cerevisiae

source_name: yeast cells genomic DNA

growth_protocol: Yeast cell were grown in YPAD medium at 30ºC to mid-log phase.

extract_protocol:
DRIP protocol was performed as described in García-Pichardo et al. 2017. Briefly, harvested cells were treated to obtain spheroplasts, genomic DNA was extracted and spooled to purify it. Fragmentation was obtained with a cocktail of restriction enzymes. A fraction of the sample was separated as input control and the rest was immunoprecipitated using S9.6 monoclonal antibody. Both immunoprecipitated (IP) and input (INP) samples were subjected to a round of whole genome amplification using a GenomePlex® Complete Whole Genome Amplification Kit from Merck, following manufacturers specifications.
Library was prepared to obtain a fragment size of 200bp according to manufacturer’s protocol for the Ion Torrent PGM (Publication Part Number 4473623 Revision Date 14 November 2011 (Rev. A)). Samples were analyzed for size, integrity and contamination with Bionalyzer and High Sensitivity DNA analysis Kit at the Genomics service in CABIMER. Run was performed in Ion 316™ Chip v2. Barcodes were added in the library preparation step in order to pool them before loading the chip.

tag: genotype

value: MATa ade2-1 bar1-delta can1-100 his3-11,15 leu2-3,112  RRM3::FLAG::KAN trp1-1 ura3::URA3/GPD-Tk(7x)

tag: cell cycle stage

value: asynchronous

tag: antibody

value: s9.6 monoclonal antibody


title: Promoter Capture Hi-C preB aged 1

tag: cell type


title: RH652-SCP-8

city: Birmingham

first: Archana

last: Sharma-Oates

address: Haworth Building

department: Centre for Computational Biology

institute: University of Birmingham

description:
The stem cell pack samples represent the left over from the stem cells that were transplanted to patients.
processed data file: merged_counts_rm_outliers.txt

data_processing:
Basecalling.
Sequenced reads were trimmed for adaptor sequence and filtered for low-quality sequence using PrinSeq v0.20.4 parameters; no_qual_header -min_len 30 -min_qual_mean 20 -ns_max_p 60 -trim_tail_right 5 -trim_tail_left 5 -trim_qual_right 20 -trim_qual_left 20 -trim_qual_type mean -trim_qual_rule lt -trim_qual_window 5
Trimmed reads were then mapped to hg19 whole genome using Star-Aligner v2.4.2a with default parameters.
Read counts were generated by HTSeq v0.6.1p1 using parameters -f bam -r name -m union -s no
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: merged_counts_rm_outliers.txt: Tab-delimited text file includes ENSEMBL gene identifiers and read counts for each sample.

source_name: PBMC

extract_protocol:
Total RNA was extracted from these FACS-sorted T cells using the Qiagen RNeasy micro kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.
The sequencing was carried out using HiSeq 2000 as 100 base paired-end reads.

treatment_protocol: T cells were flow sorted from whole PBMC.

tag: transplant type

value: allograft

tag: sample type

value: Stem cell pack

value: CD8 T cells

tag: sample identifier


title: WildType_DRIP-seq_INP

tag: strain


title: Kidney following ND_100

tag: tissue

value: Porcine kidney


title: Promoter Capture Hi-C preB young 1

value: 3 months


title: Promoter Capture Hi-C preB young 2


title: Kidney following ND_31


title: NONO PARCLIP HeLa

city: Nedlands

first: Archa

last: Fox

address: 35 Stirling Highway

country: Australia

institute: University of Western Australia

data_processing:
Cutadapt 1.8.1 was used to remove the sequencing adapters and for quality control (--max-n 0 -m 20 -q 20,20).
Sequenced reads were aligned to the human reference genome (hg38) using bowtie 1.1.1 allowing up to one mismatch, and uniquely mapped reads were retained (-v 1 -m 1).
In the uniquely mapped reads, identical reads (PCR duplicates) were collapsed.
Peaks were called using PARalyzer v1.5 with default and recommended parameters as described in the manual.
Genome_build: hg38
Supplementary_files_format_and_content: Bed files were obtained from PARalyzer (OUTPUT_CLUSTERS_FILE) including chromosome, start coordinate , end coordinate, peak ID, PARalyzer score (ModeScore), strand, T->C conversion count, read count

source_name: HeLa

growth_protocol: Both HeLa and U2OS cell lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with high glucose (4500mg/L), L-glutamine (584mg/L) and sodium pyruvate (110mg/L)(Life Technologies, cat# 11995065), and supplemented with 10% Fetal Calf Serum (Serana, cat# FBS-AU-015) and 100U/ml Penicillin/Streptomycin (Gibco, cat# 15140122). Cells were grown at 37°C in 5% CO2 in a humidified incubator.

extract_protocol:
Following UV crosslinking, cells were harvested, lysed in NP-40 lysis buffer and passed through a 32gauge needle. Lysates were cleared by centrifugation and then incubated with RNase T1 (Fermentas). Lysates were pre-cleared using Protein G Dynabeads (Invitrogen), after which RNA-protein complexes containing NONO were immunoprecipitated with NONO antibody (Monoclonal Antibody (MAb) Facility) conjugated to Protein G Dynabeads (Invitrogen). Following immunoprecipitation, beads were washed and then resuspended in dephosphorylation buffer and Calf intestinal alkaline phosphatase (New England Biolabs). Beads were then washed and incubated in polynucleotide kinase buffer and RNA was radiolabelled with Y-32P-ATP (Perkin Elmer). Radiolabelled protein-RNA complexes were removed from Dynabeads then resolved by SDS-PAGE on a NuPAGE Novex 4-12% Bis-Tris Protein Gel. Using 32P radiography RNA-protein complexes corresponding to the sizes of NONO and SFPQ  were excised from the gel, and electroeluted in D-Tube  Dialyzer  midi  tubes (Merck Millipore). Electroeluant was digested with Proteinase K (Fermentas) and RNA was then extracted from samples using miRNAeasy Micro Kit (Qiagen).
RNA extracted from PAR-CLIP was converted into a cDNA library using TruSeq small RNA Kit v2 (Illumina) with a size selection range 145-327 bp (RNA of 18-200 nt) and Illumina sequencing with 50bp single reads.

treatment_protocol: Cells were cultured in normal growth media. Prior to UV crosslinking, cells were supplemented with 4SU for 14 hours. For UV crosslinking, cells were washed with cold PBS and then irradiated with 365 nm UV at 0.15 J/cm2 in a Stratalinker 2400.

value: Immortalised cervical cancer cells

tag: passages


title: NONO PARCLIP U2OS

value: Immortalised osteosarcoma cells


title: SFPQ PARCLIP HeLa


title: Kidney following ND_01


title: SFPQ PARCLIP U2OS


title: RH652-SCP-4

value: CD4 T cells


title: Kidney following ND_47


title: Control 2: Normal magnesium low fat diet

value: epidydymal white adipose


title: RG723-wk2-8

description: processed data file: merged_counts_rm_outliers.txt

tag: time point

value: 2 weeks post-transplant


title: Hi-C preB aged 1

value: bone marrow


title: Hi-C preB young 1


title: H3K27ac ChIP-seq preB aged

value: 18-22 months

tag: chip antibody

value: H3K27ac (Abcam ab4729)


title: Hi-C preB young 2

value: flow sorted pre-B cells

value: HindIII


title: H3K27ac input aged

value: flow sorted pro-B cells


title: RG723-wk2-4


title: RG723-SCP-8


title: RCH030-wk2-8

value: autograft


title: RG723-SCP-4

value: allograft


title: RCH030-wk2-4


title: Kidney following ND_22


title: H3K27ac ChIP-seq proB aged


title: Hi-C preB aged 2


title: RB593-SCP-8

value: Stem cell pack


title: H3K27ac input young


title: H3K27ac ChIP-seq preB young


title: H3K27me3 ChIP-seq preB aged 2

value: H3K27me3 (Active Motif 39155)


title: H3K27me3 ChIP-seq preB aged 1


title: H3K27ac ChIP-seq proB young


title: LF021-wk2-8

value: CD8 T cells


title: LF021-wk2-4


title: PAR6

type: genomic

city: Baltimore

first: Hans

middle: Tomas

last: Bjornsson

state: Maryland

address: 733 N. Broadway

department: McKusick-Nathans Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
removed poorly performing probes (detection p value > 0.01); performed quantile normalization using the minfi package in R-3.1.2
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA (1125 ng) was prepared, for each sample, in a total volume of 45 μl and bisulfite treated using the EZ DNA Methylation kit (Zymo Research Corp, Orange, CA, 114 USA), as specified by the manufacturer for use with the Infinium Human Methylation 450 BeadChip arrays

tag: case status

value: case parent

tag: phenotype

value: unknown

tag: mutation

tag: Sex

value: M

tag: slide id

tag: array position


title: PAR3

value: F


title: H3K27me3 ChIP-seq proB aged 1

tag: age of mouse (months)

tag: markers


title: PAR4


title: PAR2


title: PAR1


title: KW043-wk2-8

tag: cell type


title: KW043-wk2-4

tag: transplant type

value: CD4 T cells


title: PAT8

value: case

value: KS

tag: variant classification

value: likely pathogenic


title: RB593-wk2-8

value: 2 weeks post-transplant

tag: sample identifier


title: Mf

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: CD11c- CD11b+ cells

hyb_protocol: Following fragmentation, cDNA were hybridized on Mouse Genome 430A 2.0 Array (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Genespring version 14.8using Affymetrix default analysis  (MAS 5.0) settings and global scaling as normalization method (Agilent technologies).

source_name: CD11c- CD11b+ cells

label_protocol: Fragmented and biotin-labeled cDNA was synthesized from 100 ng purified mRNA with GeneChip 3'IVT Express Kit Assay (Affymetrix).

extract_protocol: Total RNA was extracted with an RNeasy kit (Qiagen) according to the manufacturer's instructions. RNA quality was assessed by using an Agilent Bioanalyser 2100 and only RNA with minimal degradation and distinct 18S and 28S rRNA bands were used for DNA microarray analysis.

treatment_protocol: CD11chigh CD11b- DCs, CD11c- CD11b+ cells, CD11c+ CD11b+ CX3CR1high Mϕs, and CD11c+ CD11b+ CX3CR1- cells were collected from lareg intestinal lamina propria of C57BL/6J mice.

tag: strain

value: large intestine

value: CD11c- CD11b+ cells


title: RB593-wk2-4


title: CX3CR1high Mf

description: CD11c+ CD11b+ CX3CR1high Mϕs cells

source_name: CD11c+ CD11b+ CX3CR1high Mϕs cells

tag: tissue

value: CD11c+ CD11b+ CX3CR1high Mϕs cells


title: CX3CR1- DC

description: CD11c+ CD11b+ CX3CR1- cells

source_name: CD11c+ CD11b+ CX3CR1- cells

value: CD11c+ CD11b+ CX3CR1- cells


title: PAT7

value: pathogenic


title: RB593-SCP-4

value: allograft

tag: sample type

value: Stem cell pack


title: PAR5


title: KW043-SCP-8

value: autograft

value: CD8 T cells


title: PAT6


title: H3K27me3_input_preB

value: bone marrow

value: 3 months

value: flow sorted pre-B cells


title: H3K27me3 ChIP-seq proB aged 2

value: 18-22 months

value: flow sorted pro-B cells

value: H3K27me3 (Active Motif 39155)


title: H3K27me3 ChIP-seq preB young 2


title: PAT4

value: case

value: KS

value: M


title: PAT3


title: DL052-wk2-4

tag: time point

value: 2 weeks post-transplant

value: CD4 T cells


title: PAT9

value: F


title: CD103

description: CD11chigh CD11b- DCs cells

source_name: CD11chigh CD11b- DCs cells

value: large intestine

value: CD11chigh CD11b- DCs cells


title: PAT28


title: PAT26


title: H3K27me3 ChIP-seq preB young 1

tag: chip antibody


title: H3K27me3 input proB


title: PAT25

tag: case status


title: H3K27me3 ChIP-seq proB young 1


title: PAT21

tag: phenotype

value: pathogenic


title: PAT24

tag: mutation


title: PAT23

tag: Sex


title: PAT22

tag: slide id


title: AH498-SCP-8

value: allograft

value: Stem cell pack


title: DL052-SCP-4

value: autograft


title: PAT5

tag: array position


title: H3K4me3 input preB aged

value: bone marrow

tag: age of mouse (months)


title: AH498-wk2-4


title: PAT20


title: DL052-wk2-8

value: CD8 T cells


title: PAT29


title: PAT2


title: PAT19


title: PAT18


title: AH498-SCP-4


title: H3K4me3 ChIP-seq preB aged 1

value: 18-22 months

value: flow sorted pre-B cells

tag: markers

value: H3K4me3 (Active Motif 39159)


title: H3K4me3 ChIP-seq preB aged 2

tag: cell type


title: H3K4me3 input proB aged

value: flow sorted pro-B cells


title: H3K27me3 ChIP-seq proB young 2

value: 3 months

value: H3K27me3 (Active Motif 39155)


title: PAT16

value: case

value: KS


title: PAT17

value: M


title: PAT27

value: F


title: PAT15


title: DL052-SCP-8

tag: transplant type


title: PAT14

tag: variant classification


title: H3K4me3 ChIP-seq proB aged 1


title: PAT13

value: VUS (variant of unknown significance)


title: PAT12


title: H3K4me3 input preB young


title: PAT11


title: H3K4me3 ChIP-seq preB young 2


title: PAT1


title: PAT10


title: H3K4me3 ChIP-seq preB young 1


title: Con5

value: control

value: normal

value: NoneKnown


title: Con9


title: Con8


title: Con3


title: Con7


title: H3K4me3 input proB young


title: Con6


title: H3K4me3 ChIP-seq proB young 1


title: H3K4me3 ChIP-seq proB aged 2


title: Con2


title: Con4


title: ATAC-seq preB aged 4


title: Growth period 3, Phleo treated 2 [TnMP32]

city: Ann Arbor

first: Lyle

last: Simmons

state: MI

address: 830 N University Ave

department: MCDB

institute: University of Michigan

description: processed data file: MP_processed_data.csv

data_processing:
Samples were sequenced on an Illumina Hiseq 2500 using Hiseq control software-2.2.38 (TnseqMMC1-24) or 2.2.68 (TnMP1-33)
Base calling was performed using RTAVersion-1.18.61 (TnseqMMC1-24) or 1.18.66.3 (TnMP1-33)
Sequencing reads were trimmed to 43 nucleotides to remove the sequence from the transposon outside the inverted repeat
sequencing reads were mapped to PY79 genome coordinates using BWA and the reference genome "tn_site_ref.fa"
Coverage was summed for each transposon insertion site using Rstudio
Genome_build: The PY79 genome build was used to generate a transposon insertion specific reference genome; File name = "tn_site_ref.fa"
Supplementary_files_format_and_content: Processed data files include coverage for transposon insertion sites for each sample, transposon insertion site coordinate in PY79 genome (in bp), and the locus tag or gene name for each transposon insertion

organism: Bacillus subtilis PY79

source_name: Growth period 3_Phleo treated

growth_protocol:
growth conditions prior to sample extraction: Culture from growth period 2 was used to inoculate culture at OD600 equal to 0.05 and grown in the presence of 25 ng/mL Phleomycin in LB + 100 μg/mL spectinomycin to an OD600 of about 1.5
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin

extract_protocol:
Genomic DNA was isolated using a silica spin column
Sequencing libraries were constructed by digesting genomic DNA with MmeI, ligating adaptors containing illumina specific sequences, and amplifying transposon/genomic DNA junctions via PCR

treatment_protocol: Samples were treated with 15 ng/mL mitomycin C (MMC), vehicle control, 50 μg/mL methyl methane sulfonate (MMS), or 25 ng/mL phleomycin (Phleo) as indicated

tag: treatment

value: Phleo

tag: growth period

value: Growth period 3


title: Growth period 3, Phleo treated 3 [TnMP33]


title: Con1


title: ATAC-seq preB aged 3

tag: strain

tag: tissue

value: bone marrow


title: H3K4me3 ChIP-seq proB young 2


title: ATAC-seq preB aged 2

value: 18-22 months


title: Growth period 3, Phleo treated 1 [TnMP31]


title: ATAC-seq preB aged 1

value: flow sorted pre-B cells


title: Growth period 3, MMS treated 3 [TnMP30]

source_name: Growth period 3_MMS treated

growth_protocol:
growth conditions prior to sample extraction: Culture from growth period 2 was used to inoculate culture at OD600 equal to 0.05 and grown in the presence of 50 μg/mL methyl methane sulfonate in LB + 100 μg/mL spectinomycin to an OD600 of about 1.5
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin

value: MMS


title: Growth period 3, MMS treated 1 [TnMP28]


title: Growth period 3, Control 3 [TnMP27]

source_name: Growth period 3_control

growth_protocol:
growth conditions prior to sample extraction: Culture from growth period 2 was used to inoculate culture at OD600 equal to 0.05 and grown in the presence of a vehicle control in LB + 100 μg/mL spectinomycin to an OD600 of about 1.5
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin

value: Vehicle control


title: ATAC-seq proB aged 4

value: flow sorted pro-B cells


title: Growth period 3, Control 2 [TnMP26]


title: Growth period 2, Phleo treated 3 [TnMP24]

source_name: Growth period 2_Phleo treated

growth_protocol:
growth conditions prior to sample extraction: Culture from growth period 1 was used to inoculate culture at OD600 equal to 0.05 and grown in the presence of 25 ng/mL Phleomycin in LB + 100 μg/mL spectinomycin to an OD600 of about 1.5
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin

value: Growth period 2


title: ATAC-seq proB aged 3


title: Growth period 2, Phleo treated 2 [TnMP23]


title: Growth period 2, MMS treated 3 [TnMP21]

source_name: Growth period 2_MMS treated

growth_protocol:
growth conditions prior to sample extraction: Culture from growth period 1 was used to inoculate culture at OD600 equal to 0.05 and grown in the presence of 50 μg/mL methyl methane sulfonate in LB + 100 μg/mL spectinomycin to an OD600 of about 1.5
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin


title: Growth period 2, MMS treated 2 [TnMP20]


title: Growth period 2, Control 3 [TnMP18]

source_name: Growth period 2_control

growth_protocol:
growth conditions prior to sample extraction: Culture from growth period 1 was used to inoculate culture at OD600 equal to 0.05 and grown in the presence of a vehicle control in LB + 100 μg/mL spectinomycin to an OD600 of about 1.5
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin


title: ATAC-seq proB aged 2


title: Growth period 2, Control 2 [TnMP17]


title: Growth period 3, MMS treated 2 [TnMP29]


title: Growth period 2, Phleo treated 1 [TnMP22]


title: Growth period 2, MMS treated 1 [TnMP19]


title: ATAC-seq proB aged 1


title: ATAC-seq preB young 4

value: 3 months


title: Growth period 2, Control 1 [TnMP16]


title: Growth period 1, Phleo treated 3 [TnMP15]

source_name: Growth period 1_Phleo treated

growth_protocol:
growth conditions prior to sample extraction: Starter culture was used to inoculate culture at OD600 equal to 0.05 and grown in the presence of 25 ng/mL Phleomycin in LB + 100 μg/mL spectinomycin to an OD600 of about 1.5
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin

value: Growth period 1


title: E16.5_male_H3K27ac_rep1

city: Shanghai

first: Shijun

last: Shen

address: 1239 Siping Road, Shanghai, P.R. China

department: Bioninformatics

institute: Tongji University

data_processing:
ChIP–seq reads (50 bp single-end) were first trimmed of low quality and adaptor using cutadapt (v1.12), and then mapped to the mouse genome (mm10) using the bowtie (v1.2) with the parameters: -v 1 -m 1 --mm --no-unal. Uniquely mapping reads were kept for further analysis using samtools (v1.6). Signal tracks (variable step bw files) for each sample were generated using the genomeCoverageBed (from bedtools), bedSort and bedGraphToBigWig (from UCSC) The RPKM of histone modification in different region was calculated by the same method in DNase-seq.
Genome_build: mm10
Supplementary_files_format_and_content: Signal tracks (variable step bigwig files) for each sample were generated using the genomeCoverageBed (from bedtools), bedSort and bedGraphToBigWig (from UCSC)

extract_protocol:
FACS sorted Cells were first washed in 0.5% bovine serum albumin in phosphate-buffered saline (BSAPBS, Sigma) solution to avoid potential contamination. After washing, fresh cells were collected in 1.5 ml tubes and resuspended in 45μl lysis buffer (40 mM Tris-HCl, pH 7.5, 10 mM NaCl, 6 mM MgCl2, 6 mM CaCl2, 0.1% NP40) then incubated on ice for 5 min to release the nuclei. DNase I (10,000 U/ml, Roche, 04716728001) was added to the final concentration of 30 U/ml, and incubated at 37 °C for exactly 5 min. DNase I concentrations to achieve optimal smearing sizes may differ for each cell line and therefore should be determined empirically for each cell type. After DNase I digestion, the reaction was terminated immediately by adding 50μl Stop Buffer (40 mM Tris-HCl, pH 7.5, 10 mM NaCl, 0.5% SDS, 10 mM EDTA) containing 1μl Proteinase K (20 mg/ml, Life Technologies). After incubation at 55 °C for 1h, DNA was purified by extraction with phenol–chloroform and precipitated by ethanol in the presence of glycogen (20 mg/ml, Roche, 10901393001) more than 3 hours at −20 °C.  The sequence libraries were generated using the KAPA Hyper Prep Kit for the Illumina platform (kk8504), following the manufacturer’s instructions. In order to evaluate the library complexity, we chose agarose gel electrophoresis instead of SPRI-beads based methods for size selection. Because DNase I hypersensitive sites are not binary, only the smearing pattern samples were ideal for generating high-quality DNase data. DNA fragments of 150-300bp were extracted from the agarose gel for a second PCR amplification. The DNA was eluted in 15μl of elution buffer (2.5 mM Tris, pH 7.6, 0.05 mM EDTA) and quantified by a Qubit dsDNA HS assay kit (Thermo Fisher Scientific, Q32854) and Agilent High Sensitivity assay kit (Agilent Technologies). The libraries were sequenced on a Hiseq2500 with single-end 50bp reads (Illumina).
The sequence libraries were generated using the KAPA Hyper Prep Kit according to the manufacturer’s instructions. The libraries were sequenced on a Hiseq2500 with single-end 50bp reads (Illumina).

treatment_protocol: For mouse PGCs, male mice homozygous for Oct4-EGFP transgene on an inbred C57BL/6J background were crossed with wild-type C57BL/6 females. Noon of the day when a copulatory plug was evident was counted as E0.5. For E12.5 experiments, embryos were genotyped to conﬁrm sex, and then gonads of each sex were pooled for ﬂow cytometry. For E13.5 and E14.5 experiments, male and female gonads were identiﬁed by the presence or absence of testicular cords, and gonads of each sex were pooled. Gonads were treated with 0.25% Trypsin-EDTA for 10 min at 37 °C, and trypsin was inactivated by addition of 15% Fetal Bovine Serum (FBS)/ DMEM. Cells were filtered through 40 µm cell strainers to obtain single cell suspension for FACS sorting (FACS Aria II SORP, BD Bioscience).

value: primordial germ cell

tag: development stage

tag: gender

value: male

value: H3K27ac, Active Motif, #39133

tag: genotype

value: wild type


title: Growth period 1, Phleo treated 2 [TnMP14]


title: Growth period 1, Phleo treated 1 [TnMP13]


title: ATAC-seq preB young 2


title: Morula.IVF.Input

city: Hangzhou

first: Li

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

data_processing:
Downloaded ChIP-seq and DIP-seq reads, as well as H3K27-3 ULI-NChIP-seq reads generated in this study, were mapped to the mouse genome (mm9) using Bowtie (version 2.1.0) with parameters “-D 20 -R 3 -N 1 -L 20 -i S,1,0.50” to obtain only those reads that are mapped uniquely with at most 3 mismatches. Peak calling of H3K27me3 ChIP-seq data was performed using macs2 (version 2.1.1) with parameters “--broad --nomodel --nolambda --down-sample --broad-cutoff  0.01”. To visualize the signals in the genome browser, we generated wig track files for each data set with MACS2 (version 2.1.1) by extending the uniquely mapped reads (keeping at most two read at the same genomic position) to 200 bp toward the 3’ end and binning the read count to 50 bp intervals. Tag counts were further normalized in each bin to the total number of uniquely mapped reads (reads per million reads, RPM). The ‘computeMatrix’ program from deepTools was used to compute the ChIP-seq and DIP-seq signals over the DMRs or ICRs and their flanking regions.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files for ChIP-seq data

source_name: early embyro

extract_protocol:
SCNT embryos were generated from Sertoli cells of Xist heterozygous knockout pups in BDF1 x PWK hybrid genetic background through Kdm4d mRNA injection. IVF embryos were generated using BDF1 oocytes and PWK sperm. Fifty to sixty IVF or SCNT embryos at the morula stage were collected at 72 hpa and pooled as a single sample with biological replicates. After digestion of zona pellucida by acid Tyrode’s solution, polar bodies were removed by brief treatment with 0.25% trypsin 1 mM EDTA followed by several times of quick pipetting. The embryos were then washed three times with PBS containing 0.2% BSA (Merck # 12657) and processed for chromatin isolation and fragmentation by Micrococcal Nuclease (MNase: New England Biolabs # M0247S). 10 % of MNase-treated chromatin solution was used as input. Rabbit anti-H3K27me3 antibody (Diagenode # C15410069) was used for immunoprecipitation.
Sequencing libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs # E7645S) following manufacturer’s instructions.

value: Morula embyro

value: BDF1 X PWK


title: Morula.SCNT.Input


title: ATAC-seq preB young 1

source_name: bone marrow


title: Growth period 1, MMS treated 3 [TnMP12]

source_name: Growth period 1_MMS treated

growth_protocol:
growth conditions prior to sample extraction: Starter culture was used to inoculate culture at OD600 equal to 0.05 and grown in the presence of 50 μg/mL methyl methane sulfonate in LB + 100 μg/mL spectinomycin to an OD600 of about 1.5
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin


title: Growth period 1, MMS treated 2 [TnMP11]


title: Growth period 1, MMS treated 1 [TnMP10]


title: ATAC-seq preB young 3


title: ATAC-seq proB young 4


title: Growth period 3, Control 1 [TnMP25]


title: Morula.SCNT.H3K27me3.Rep2


title: Growth period 1, Control 3 [TnMP9]

source_name: Growth period 1_control

growth_protocol:
growth conditions prior to sample extraction: Starter culture was used to inoculate culture at OD600 equal to 0.05 and grown in the presence of a vehicle control in LB + 100 μg/mL spectinomycin to an OD600 of about 1.5
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin


title: Morula.SCNT.H3K27me3.Rep1


title: ATAC-seq proB young 3


title: Growth period 1, Control 2 [TnMP8]


title: Morula.IVF.H3K27me3.Rep2


title: ATAC-seq proB young 2


title: MMS & Phleo Starter Culture 3 [TnMP6]

source_name: MMS & Phleo Starter Culture 3

growth_protocol:
growth conditions prior to sample extraction: Transposon insertion library grown to OD600 of about 0.8 in LB + 100 μg/mL spectinomycin
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin

value: Starter culture

value: none; Starter culture


title: MMS & Phleo Starter Culture 1 [TnMP4]

source_name: MMS & Phleo Starter Culture 1


title: MMS & Phleo Library 2 [TnMP2]

source_name: MMS & Phleo Library 2

growth_protocol:
growth conditions prior to sample extraction: Transposon insertion library isolated from LB agar plates containing 100 μg/mL spectinomycin to select for cells with a transposon
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin

value: Transposition library

value: none; Transposition library


title: ATAC-seq proB young 1

value: bone marrow


title: MMS & Phleo Library 3 [TnMP3]

source_name: MMS & Phleo Library 3


title: MMS & Phleo Starter Culture 2 [TnMP5]

source_name: MMS & Phleo Starter Culture 2


title: Morula.IVF.H3K27me3.Rep1


title: Nuclear RNA-seq proB aged 2

description:
Nuclear RNA
Nuclear_RNA_counts.txt

value: 18-22 months


title: SCNT_methylation

data_processing:
Bisulfite-seq reads reads were first trimmed using trim_galore to remove low-quality sequences and adapter sequences. Bismark (version 0.15.0) was used to align reads to a bisulfite converted reference genome (mm9). The coverage depth and methylation level of each cytosine were extracted from the aligned reads with bismark_methylation_extractor. When calculating methylation level for CpG sites, information from both strands was combined, and a coverage of at least five reads was required.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph format with tab-separated values (chr, CG_start, CG_end, methyaltion_score, methylated_CG_num, unmethylated_CG_num).

source_name: mouse blastocysts generated with somatic nuclear transffer

growth_protocol: B6D2F1/J (BDF1) mice were used for the collection of recipient oocytes for SCNT. For mouse embryonic fibroblast (MEF) cell preparation, Xist KO female mice maintained in 129S1/SvImj background (Marahrens et al., 1997) were mated with CAST/EiJ males to generate Xist heterozygous KO embryos in 129/CAST F1 background. Somatic cell nuclear transfer was carried out as described previously (Matoba et al., 2014; Ogura et al., 2000). IVF was performed using Xist KO oocytes (129S1/Svj background) and WT sperm (CAST/EiJ background)

extract_protocol:
IVF and SCNT embryos of the early blastocyst stage (96 hours after fertilization or activation) were directly subjected to bisulfite conversion using the EZ DNA Methylation-Direct Kit (Zymo Research, D5020). Thirty-nine and 36 embryos were used for preparing the IVF and SCNT samples, respectively. A small amount (0.01 ng) of unmethylated Lambda DNA (Promega, D152A) was added to each sample before bisulfite conversion to serve as spike-in controls for evaluating bisulfite conversion efficiency.
Sequencing libraries were prepared using the EpiGnome Methyl-Seq kit (Epicenter, EGMK81312) following the manufacturer’s instructions. Libraries were only amplified for 12 cycles, and were then purified using Agencourt AMPure XP beads (Beckman Coulter, A63880). Final libraries were subjected to single-read (100 bp) sequencing on a HiSeq 2500 sequencer (Illumina) with PhiX spike-in control.

value: blastocysts

tag: generation method

value: somatic nuclear transfer

value: 129S1/Svj x CAST/EiJ

value: Xist-KO


title: MMS & Phleo Library 1 [TnMP1]

source_name: MMS & Phleo Library 1


title: IVF_methylation

source_name: mouse blastocysts generated with in vitro fertilization

value: in vitro fertilization


title: Growth period 3, MMC treated 3 [TnseqMMC24]

description: processed data file: MMC_processed_data.csv

source_name: Growth period 3_MMC treated

growth_protocol:
growth conditions prior to sample extraction: Culture from growth period 2 was used to inoculate culture at OD600 equal to 0.05 and grown in the presence of 15 ng/mL mitomycin C in LB + 100 μg/mL spectinomycin to an OD600 of about 1.5
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin

value: MMC

value: Growth period 3


title: CTCF input preB aged

value: flow sorted pre-B cells


title: Nuclear RNA-seq proB aged 1

description:
Nuclear RNA
Nuclear_RNA_counts.txt

value: flow sorted pro-B cells


title: CTCF ChIP-seq preB aged 2

tag: chip antibody

value: CTCF (Millipore 07-729)


title: Growth period 3, MMC treated 2 [TnseqMMC23]


title: Nuclear RNA-seq proB young 2

description:
Nuclear RNA
Nuclear_RNA_counts.txt

value: 3 months


title: Growth period 1, Control 1 [TnMP7]

value: Vehicle control

value: Growth period 1


title: NaSi rep2

city: Yangling

first: Ruolin

last: Yang

state: Shaanxi

address: No.3 Taicheng Road

institute: Northwest A&F University

description: Cucumber leaves from salt and silicon treated seedlings

data_processing:
Sequenced clean reads were mapped to cucumber genome (v2) using TopHat2 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated according to the protocol (Trapnell et al., Nature protocols, 2012).
Genome_build: GCF_000004075.2
Supplementary_files_format_and_content: txt files showing the RPKM values of genes for each Sample

organism: Cucumis sativus

source_name: leaves

growth_protocol: Cucumber (Cucumis sativus L. ‘JinYou 1’) seeds were rinsed thoroughly in distilled water and germinated on moist gauze in an incubator at 28 °C for 2 days. The germinated seeds were sown in quartz sands in a greenhouse with a day/night temperature of 28℃/18℃. The seedlings were transferred to 15-L plastic containers filled with 1/4 strength of modified Hoagland nutrient solution at two-leaf stage. Three days later, the strength of Hoagland solution was increased to 1/2.

extract_protocol:
Total RNA was harvested using Trizol reagent following manufacture`s protocol (Roche, Mannheim, Germany).
RNA-Seq library construction and sequencing were conducted by Gene Denovo Co. (Guangzhou, China). The poly(A)-containing mRNA molecules were purified from 10 mg of total RNA using poly-T oligo-attached magnetic beads. The extracted mRNAs were fragmented into 200-bp-long pieces using RNA Fragmentation Buffer (Kapa, Biosystems). The cleaved Illumina Sequencing mRNA fragments were reverse-transcripted into first-strand cDNA using random primers, followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. Then, the cDNA fragments went through an end repair process, the addition of a single “A” base, and ligation of the adapter sequences. Finally, the cDNA products were purified and enriched to construct libraries for non-strand-specific RNA-Seq.

treatment_protocol: Seven days after transplanting, silicon (0.3 mM) and salt (75 mM) treatment were started by adding sodium silicate (Na2SiO3·9H2O) and sodium chloride (NaCl) to the nutrient solution. There were four treatments: control (CT), silicon treatment (Si), salt stress (NaCl), and salt stress plus silicon (NaSi). The pH of nutrient solution was adjusted to 6.0 using 0.2 M H2SO4 or 1 M KOH. Three days after salt and silicon treatment, the recently fully expanded leaves were collected with every 3 of them being mixed as one biological replicate for each treatment. Every treatment had 3 biological replicates, except silicon treatment alone, which had 2 replicates.

tag: cultivar

value: JinYou 1

value: leaves

tag: condition

value: salt and silicon treated


title: NaSi rep3


title: Growth period 3, MMC treated 1 [TnseqMMC22]


title: Growth period 3, Control 3 [TnseqMMC21]

source_name: Growth period 3_control


title: Total RNA-seq preB aged 3

description:
Total RNA depleted for rRNA
Total_RNA_counts.txt

growth_protocol: All cells were depleted of non-B lineage cells by magnetic cell sorting, and then flow sorted for pro-B and pre-B cells, directly from bone marrow single cell suspensions from young and aged mice

value: bone marrow

value: 18-22 months


title: NaSi rep1


title: CTCF ChIP-seq preB aged 1


title: CTCF input preB young


title: Nuclear RNA-seq proB young 1

description:
Nuclear RNA
Nuclear_RNA_counts.txt


title: Growth period 3, Control 2 [TnseqMMC20]


title: Si rep2

description: Cucumber leaves from silicon treated seedlings

value: silicon treated


title: Si rep1


title: Total RNA-seq preB aged 1


title: Total RNA-seq preB aged 2


title: CTCF ChIP-seq preB young 2


title: CTCF ChIP-seq preB young 1


title: Na rep3

description: Cucumber leaves from salt stressed seedlings

value: salt stressed


title: Growth period 2, MMC treated 2 [TnseqMMC17]

source_name: Growth period 2_MMC treated

growth_protocol:
growth conditions prior to sample extraction: Culture from growth period 1 was used to inoculate culture at OD600 equal to 0.05 and grown in the presence of 15 ng/mL mitomycin C in LB + 100 μg/mL spectinomycin to an OD600 of about 1.5
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin

value: Growth period 2


title: MicroRNA-seq preB aged 4

description:
small RNA
MicroRNA_counts.txt


title: Growth period 3, Control 1 [TnseqMMC19]


title: Total RNA-seq proB aged 3


title: Growth period 2, MMC treated 3 [TnseqMMC18]


title: Total RNA-seq proB aged 2


title: Total RNA-seq proB aged 1


title: MicroRNA-seq preB aged 3

description:
small RNA
MicroRNA_counts.txt


title: Na rep1


title: Growth period 2, Control 3 [TnseqMMC15]

source_name: Growth period 2_control


title: Growth period 2, MMC treated 1 [TnseqMMC16]


title: MicroRNA-seq preB aged 2

description:
small RNA
MicroRNA_counts.txt


title: Growth period 2, Control 2 [TnseqMMC14]


title: Control rep3

description: Cucumber leaves from control seedlings

value: control


title: Na rep2


title: Total RNA-seq preB young 2


title: Control rep2

description: Cucumber leaves from control seedlings


title: Total RNA-seq preB young 1


title: Control rep1

description: Cucumber leaves from control seedlings


title: MicroRNA-seq preB aged 1

description:
small RNA
MicroRNA_counts.txt


title: Growth period 1, MMC treated 3 [TnseqMMC12]

source_name: Growth period 1_MMC treated

growth_protocol:
growth conditions prior to sample extraction: Starter culture was used to inoculate culture at OD600 equal to 0.05 and grown in the presence of 15 ng/mL mitomycin C in LB + 100 μg/mL spectinomycin to an OD600 of about 1.5
Samples were grown at 30°C in LB + 100 μg/mL spectinomycin

value: MMC


title: Growth period 1, MMC treated 2 [TnseqMMC11]


title: MicroRNA-seq proB aged 3

description:
small RNA
MicroRNA_counts.txt

source_name: bone marrow


title: Total RNA-seq proB young 3


title: AVF-CKD 5

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

institute: The Mayo Clinic

data_processing:
TopHat v2.1.0 for alignment
FeatureCounts to quantify expression
edgeR for defining differentially expressed genes
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv format containg raw gene counts and RPKM normalize expression values

source_name: venous limb of AVF

extract_protocol:
trizol and Qiagen total RNA kit
TruSeq RNA Sample Prep Kit v2

treatment_protocol: sham and AVF-CKD surgery

tag: time point

value: harvested 7 days after surgery

tag: protocol

value: AVF-CKD surgery


title: MicroRNA-seq proB aged 2

description:
small RNA
MicroRNA_counts.txt

tag: age of mouse (months)

value: flow sorted pro-B cells

tag: markers


title: AVF-CKD 6


title: AVF-CKD 4


title: Growth period 1, MMC treated 1 [TnseqMMC10]


title: Total RNA-seq proB young 2

tag: cell type


title: MicroRNA-seq proB aged 1

description:
small RNA
MicroRNA_counts.txt


title: Growth period 1, Control 3 [TnseqMMC9]

source_name: Growth period 1_control


title: AVF-CKD 3


title: Total RNA-seq proB young 1


title: MicroRNA-seq preB young 3

description:
small RNA
MicroRNA_counts.txt

value: flow sorted pre-B cells


title: MicroRNA-seq preB young 4

description:
small RNA
MicroRNA_counts.txt

value: 3 months


title: Total RNA-seq preB young 3


title: Growth period 1, Control 1 [TnseqMMC7]

value: Vehicle control


title: Growth period 1, Control 2 [TnseqMMC8]

value: Growth period 1