title: pNSC_2D_ab42_R2

source_name: 2D cell culture


title: WBJPE171125081

status: Public on Jan 01 2020

type: SRA

city: Hangzhou

first: Yixiao

last: Liu

state: 浙江

address: Yuhangtang road

country: China

institute: Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Single-cell RNA sequence reads were evaluated by FastQC
Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than 20.
The reads were mapped to the mm9 using bowtie2.
The mapped reads for genes were counted via Htseq.

molecule: total RNA

organism: Mus musculus

source_name: skeleton muscle

extract_protocol:
Cells were isolated by preplating mehods (Nat. Protocols 3, 1501-1509 (2008)).
single cell were captured, lysated, preamplified and library prepared according to "Using the C1 High-Throughput IFC to Generate Single-Cell cDNA Libraries for mRNA Sequencing"

treatment_protocol: 563 mice skeletal muscle derived single cells were form  6~8 weeks old male C57BL/6 mice.

tag: tissue

value: mice skeletal muscle

tag: strain

tag: gender

value: male


title: pNSC_3D_Ctrl_R1

city: New York

first: Caghan

last: Kizil

state: NY

country: USA

institute: Columbia University Irving Medical Center

description: Papadimitriou_2017_featureCounts_table.s2.tab

data_processing:
The FastQ files were aligned to human genome (GRCh38/hg19) using gsnap (2016-0923) with default options. The read counts for each gene were calculated using featureCounts (V1.5.3) and GTF file from ensemble genome browser (Homo_sapiens.GRCh38.90.gtf).
Genome_build: GRCh38/hg19
Supplementary_files_format_and_content: The processed data file contains read counts calculated by featureCounts. The first 6 columns contain information about the gene (Geneid, Chr, Start, End, Strand, Length), and the remaining columns countain read counts of each gene in each sample. The colnames have not been changed and contain Raw Files names with additional suffix ".gz.sam"

organism: Homo sapiens

source_name: 3D cell culture

growth_protocol: Primary human neural stem cells (human cortical astrocytes) from fetus, gestation week 21, obtained from ScienCell Reaserch Laboratory (SRL) (Cat#1800) at passage one and delivered frozen. The HCCs are seeded on conventional T75 flasks or 24-well plates and cultured using Astrocyte medium (SRL, Cat No. 1801) supplemented with 5% of fetal bovine serum (SRL, Cat. No.0010), 1% of astrocyte growth supplement (SRL,Cat. No. 1852) and 1% of penicillin/streptomycin solution (SRL, Cat. No. 0503) in an incubator with an atmosphere of 5% CO2/95% air and 37 °C. Induced human neural stem cells (HIP, BC1 line, Amsbio, Cat No. GSC-4311) were thawed and cultured for expansion using Geltrex precoating of flasks according to manufacturer’s instructions. The medium used for expansion and further culturing was the “expansion medium” formulation according to the manufacturer’s instructions. NeuralX™ NSC Medium; 2% GS22™ Neural Supplement 10; 1X Non-Essential Amino Acids, 2mM L-alanine/L-glutamine; 20 ng/ml FGF2 were used. The gels were cultured and incubated in 5% CO2/95% air at 37 °C.

extract_protocol:
For 2D cells; Human fetal cortical cells were grown in monolayer. Firstly we rinsed cell monolayer with ice cold PBS once. WE add 500 ul of TRIZOL reagent to lyse cells directly in a 24 well culture dish and scrape with a cell scraper. Pass the cell lysate several times through a pipette and then we vortex thoroughly. Add 0.2 ml of chloroform per 1 ml of TRIZOL. Vortex samples for 15 seconds and incubate them at room temperature for 2 to 3 minutes. Centrifuge the samples at 12,000 x g for 15 minutes at room temperature. Transfer upper aqueous phase into fresh RNAse-free tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIZOL used for the initial homogenization. Incubate samples at room temperature for 10 minutes and centrifuge at 12,000 x g for 10 minutes at 4oC. Remove the supernatant completely. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIZOL Reagent used for the initial homogenization. Mix the samples by vortexing and centrifuge at 7,500 x g for 5 minutes at 4oC. Repeat above washing procedure once. Remove all leftover ethanol. Air-dry or vacuum dry RNA pellet for 5-10 minutes. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip. For cells from 3D gels, we used Norgen Total RNA Isolation Kit. RNA isolation performed according to the protocol suggest by the company except; 3 gels lysed in 1ml RL buffer with 10 µL beta-mercaptoethanol. Centrifuged at 10000g for 5 min at RT and supernatant (~930 µL) transfered to a new eppendorf. 580 µL %96-99 ethanol added and mixed throughly. After passing through samples on columns, washings and DNase I treatment done accroding to the protocol suggests and RNA eluted in50 µL  nuclease free water. Samples ran on Agilent Bioanalyser for RNA quality, samples with RNA integrity >= 9.0 used for library preparation.
Total RNA with an integrity number of ≥ 8 was used. mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module. After chemical fragmentation by incubating for 15 min at 94°C the sample was directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB)

treatment_protocol: 2D cultures were treated with 2 uM Abeta42 in the culture medium for 2 days between 2 and 4 days of culture. The medium is removed and cells are washed with cell culture medium twice. Amyloid plaques remain in the culture attached to the cells throughout the cultures. New medium is added and cultures were continued. For 3D cultures, Abeta42 is mixed with heparin solution at the time the gels are prepared. Cultures are performed for three weeks with frequent media changes.

tag: cells

value: Human Cortical Astrocytes from human fetal cortex

tag: culture medium

tag: treatment

value: control


title: WBJPE171125080


title: KLRG1_GFP_plus Replicate 3 [scRNA-seq]

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

country: Germany

institute: University Medical Center of the Johannes Gutenberg-University Mainz

data_processing:
Fastq files were processed using Cell Ranger version 2.0.1 based on 10xGenomics provided mm10 reference genome (refdata-cellranger-mm10-1.2.0). Cell Ranger was run per sample (using cellranger count). For downstream analysis the R package Seurat (version 2.3.0) together with R (version 3.4.2) was used. Cells with less than 500 or more than 2500 transcripts were discarded as well as cells exceeding a 5% threshold of mitochondrial transcripts. The data was log normalized (using NormalizeData) and scaled (using ScaleData) which includes regressing for mitochondrial DNA content and the number of UMIs using a negative binomial distribution. Highly variable genes (HVGs) were identified (using FindVariableGenes) with default parameter settings. TSNE (using RunTSNE) was used for dimensionality reduction and visualization.   To reconstruct a developmental trajectory, Monocle (version 2.6.3) was used. Steps included size factor estimation (using estimateSizeFactors), estimation of dispersions (using estimateDispersions), applying a minimal expression threshold of 0.1 (using detectGenes), HVGs were set to be used (using setOrderingFilter) and reducing dimensionality to two components (using setOrderingFilterreduceDimension(method = ‘DDRTree’) ). For visualization purpose, cells were binned in hexagons and expression was calculated as a mean based on the gene of interest.   Pearson correlation was calculated on HVGs of precursor tisTregST2 cells. 30 most correlated and anti-correlated genes to Batf were clustered using pheatmap and R (version 3.4.2) with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx, h5

source_name: Spl Klrg1negNfil3pos Treg

growth_protocol: Mice were housed at DKFZ or UKR central animal facility

extract_protocol: Samples for scRNA-seq were loaded on the Chromium Single cell Controller (10x Genomics #120212) using the Single Cell 3' Library & Gel Bead Kit v2 (10x Genomics #120237). cDNA was amplified using 14 cycles of PCR. Library was constructed using 13 cycles of PCR. Products were purified using Ampure XP beads and quality was controlled using Agilent Tapestation.

treatment_protocol: T cells were isolated and pre-enriched as described in the associated publication. Afterwards, they were stained with live/dead dye and surface antibodies as described. Cells were then sorted on an BDTM FACSAriaTM IIu, III, or FACSAriaTM FUSION cell sorter using 70 µm or 85 µm nozzle size and 4-way-purity sort mode into 1.5 ml tubes filled with FACS buffer. Sample and post-sort quality control were recorded where applicable and are displayed in the source data file linked to this manuscript. For scRNA-seq, we sorted 15000 spleen CD25+Klrg1-Nfil3(GFP)- Treg, 15000 spleen CD25+Klrg1-Nfil3(GFP)+ Treg, 15,000 spleen CD25+Klrg1+Nfil3(GFP)+ Treg, 10000 spleen CD44+CD25+Foxp3(GFP)+ Treg, 7500 VAT CD44+CD25+Foxp3(GFP)+ Treg, 3000 skin CD44+CD25+Foxp3(GFP)+ Treg, 1500 blood CD44+CD25+Foxp3(GFP)+ Treg, 10000 inguinal lymph-node CD44+CD25+Foxp3(GFP)+ Treg, 10000 bone marrow CD44+CD25+Foxp3(GFP)+ Treg, 10000 lung CD44+CD25+Foxp3(GFP)+ Treg, and 1000 liver CD44+CD25+Foxp3(GFP)+ Treg. Samples were pooled from several Foxp3(GFP) or Foxp3(YFP) or Nfil3(GFP) reporter mice.

tag: cell type

value: Klrg1-negative Nfil3(GFP)-positive


title: pNSC_2D_Ctrl_R2


title: KLRG1_GFP_plus Replicate 2 [scRNA-seq]


title: KLRG1_GFP_plus Replicate 1 [scRNA-seq]


title: pNSC_2D_ab42_R1

value: 2 uM Abeta42


title: WBJPE171125079


title: mut CH12+(C-terminus+11ZFs of CTCF)

city: Bethesda

first: Elena

last: Pugacheva

state: MD

department: NIAID

institute: NIH

description: mutant

library_source: genomic

data_processing:
Hi-C reads (paired end, 50 bases) were aligned against the mm9 genome using BWA-mem.
PCR duplicate reads were removed using Picard MarkDuplicates.
We used juicebox to create hic file with -q 30 -f options and to visualize Hi-C data.
The aggregate analysis of chromatin loops was performed using Aggregate Peak Analysis (APA) with default parameters and 10 kb resolution.
Genome_build: mm9
Supplementary_files_format_and_content: hic files for visualizion of Hi-C data.

molecule: genomic DNA

source_name: Mouse B lymphoma cell

growth_protocol: CH12F3 (CH12) B lymphoma cell line was maintained in RPMI 1640 supplemented with 10% FBS, 1% penicillin/streptomycin and 55 μM 2-β mercaptoethanol.

extract_protocol:
In situ Hi-C experiments were performed using the MboI restriction enzyme. The crosslinked pellets (1.5 million cells) were incubated and washed with 200 μL of lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630, 33 μL Protease Inhibitor (Sigma, P8340)) on ice, and then incubated in 50 μL of 0.5% SDS for 10 min at 62°C. After heating, 170 μL of 1.47% Triton X-100 was added and incubated for 15 min at 37˚C. To digest chromatin 100 U MboI and 25 μL of 10X NEBuffer2 were added followed by overnight incubation at 37˚C. The digested ends were filled and labeled with biotin by adding 37.5 μL of 0.4 mM biotin-14-dATP (Life Tech), 1.5 μL of 10 mM dCTP, 10 mM dTTP, 10 mM dGTP, and 8 μL of 5 U/μL Klenow (New England Biolabs) and incubating at 23°C for 60 minutes with shaking at 500 rpm on a thermomixer. Then the samples were mixed with 1x T4 DNA ligase buffer (New England Biolabs), 0.83% Triton X-100, 0.1 mg/mL BSA, 2000 U T4 DNA Ligase (New England Biolabs, M0202), and incubated for at 23°C for 4 hours to ligate the ends. After the ligation reaction, samples were resuspended in 550 μL 10 mM Tris-HCl, pH 8.0. To reverse the crosslinks, 50 μL of 20 mg/mL Proteinase K (New England Biolabs) and 57 μL of 10% SDS were mixed with the samples, and incubated at 55°C for 30 minutes, and then 67 μL of 5 M NaCl were added followed by overnight incubation at 68°C. After cooling at room temperature, 0.8X Ampure (Beckman-Coulter) purification was performed, and the samples were sonicated to a mean fragment length of 400 bp using Covaris M220. Two rounds of Ampure (Beckman-Coulter) beads purification was performed for size selection.
Biotin-labeled DNA was purified using Dynabeads MyOne T1 Streptavidin beads (Invitrogen). The beads were washed with 400 μL of 1x Tween Wash Buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), and resuspended in 300 μL of 2x Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl). The beads were added to samples and incubated for 15 minutes at room temperature. Then the beads were washed twice by adding 600 μL of 1x Tween Wash Buffer. Then the beads were equilibrated once in 100 uL 1x NEB T4 DNA ligase buffer (New England Biolabs) followed by removal of the supernatant using a magnetic rack. To repair the fragmented ends, the beads were resuspended in 100 μL of the following: 88 μL 1X NEB T4 DNA ligase buffer (New England Biolabs, B0202), 2 μL of 25 mM dNTP mix, 5 μL of 10 U/μL T4 PNK (New England Biolabs), 4 μL of 3 U/μL NEB T4 DNA Polymerase (New England Biolabs), 1 μL of 5 U/μL Klenow (New England Biolabs). The beads were incubated for 30 minutes at room temperature. The beads were washed twice by adding 600 μL of 1x Tween Wash Buffer. To add a dA-tail, the beads were resuspended in 100 μL of the following: 90 μL of 1X NEBuffer2, 5 μL of 10 mM dATP, and 5 μL of 5 U/μL Klenow (exo-) (New England Biolabs). The beads were incubated for 30 minutes at 37˚C. The beads were washed twice by adding 600 μL of 1x Tween Wash Buffer. Following the washes, the beads were equilibrated once in 100 μL 1x NEB Quick Ligation Reaction Buffer (New England Biolabs) and the supernatants were removed using a magnetic rack. The beads were then resuspended in 50 μL 1x NEB Quick Ligation Reaction Buffer. To ligate adapters, 2 μL of NEB DNA Quick Ligase (New England Biolabs) and 3 μL of Illumina Indexed adapter were added to the beads and incubated for 15 minutes at room temperature. The supernatant was removed and the beads were washed twice by adding 600 μL of 1x Tween Wash Buffer. Then the beads were resuspended once in 100 μL 10 mM Tris-HCl, pH 8.0, followed by removal of the supernatant and resuspension again in 50 μL 10 mM Tris-HCl, pH 8.0. After deciding an optimal PCR cycle number using KAPA DNA Quantification kit (Kapa Biosystems), 6 cycles of PCR amplification were performed with the following reaction mixture: 10 μL Phusion HF Buffer (New England Biolabs), 3.125 μL 10 μM TruSeq Primer 1, 3.125 μL 10 μM TruSeq Primer 2, 1 μL 10 mM dNTPs, 0.5 μL Fusion HotStartII, 20.75 μL ddH20, 11.5 μL Bead-bound Hi-C library. PCR products were subjected to a final purification using AMPure beads (Beckman-Coulter) and were eluted in 30 μL 10 mM Tris-HCl, pH 8.0. Libraries were sequenced on the Illumina HiSeq 4000 platform.

tag: expressed vector

value: ORF of C-terminus and 11ZFs of CTCF inserted into pMy-MouseCTCFbiotag-T2A-mOrange

tag: genotype

value: homozygous deletion of ZF9-11 in CTCF gene


title: WBJPE171125078


title: KLRG1_plus_GFP_plus Replicate 4 [scRNA-seq]

source_name: Spl Klrg1posNfil3pos Treg

value: Klrg1-positive Nfil3(GFP)-positive


title: pNSC_2D_Ctrl_R1


title: WBJPE171125077


title: KLRG1_plus_GFP_plus Replicate 3 [scRNA-seq]


title: P493_MST

city: Singapore

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*Star Singapore

data_processing:
Illumina Casava v1.8 used for basecalling.
Sequences were mapped to hg19 using bowtie2 v2.2.3 with parameters -N 0 --sensitive --no-unal -q -U
MACS v2.0.10.20131216 was used for peak calling with parameters --llocal=10000 -g 3095677412 --bw 200 --shiftsize 100 -f BAM -p 0.05 --slocal=1000 --keep-dup=3 --nomodel
Genome_build: hg19
Supplementary_files_format_and_content: MACS v2.0.10.20131216 peaks file

source_name: P493 MST

growth_protocol: P493 cells were maintained in RPMI medium 1640 supplemented with 10% FBS, penicillin, penicillin and streptomycin.

extract_protocol:
Cells were treated with 1% formaldehyde for 10 minutes at room temperature to crosslink protein-DNA complexes, and reactions were then quenched using 125 mM glycine for 5 minutes. The cells were then lysed with sodium dodecyl sulfate (SDS) lysis buffer and sonicated for 10 minutes using the Diagenode Bioruptor. The fragmented chromatin was pre-cleared with bovine serum albumin (BSA), protein A Sepharose beads (Millipore) at 4 ˚C for 2 hours before immunoprecipitation with c-MYC or rabbit control IgG antibodies overnight at 4 ˚C. Sepharose beads were washed as described previously and eluted with SDS elution buffer before subjecting to reverse cross-linking at 65 ˚C overnight. Finally samples were purified using the QIAquick PCR Purification Kit (Qiagen) according to the manufacturer’s protocol.
Single read - Illumina

tag: cell line

tag: chip antibody

value: anti-Myc (Santa Cruz Biotechnology, Catalog#:sc-764, Antibody name:N262, Lot#:D0413)


title: gDNA from normal human bone marrow RO02176

type: genomic

city: Little Rock

first: Jason

middle: Eli

last: Farrar

state: AR

address: 1 Children's Way, #512-10

department: Pediatrics/Hematology-Oncology

institute: University of Arkansas for Medical Sciences

hyb_protocol: Bisulfite-converted genomic DNA was analyzed using the Infinium Human Methylation EPIC Beadchip Kit (Illumina). DNA amplification, fragmentation, array hybridization, extension and staining were performed with reagents provided in the kit according to the manufacturer’s protocol (Illumina Infinium II Methylation Assay). Briefly, 4 µl of bisulfite-converted genomic DNA at a minimum  concentration of 20 ng/µL) was added to 0.8 ml 96-well storage plate (Thermo Fisher Scientific), denatured in 0.014N sodium hydroxide, neutralized and then amplified for 20-24 hours at 37oC. Samples were fragmented at 37oC for 60 minutes and precipitated in isopropanol. Re-suspended samples were denatured in a 96-well plate heat block at 95oC for 20 minutes. 15 µl of each sample was loaded onto a 12-sample BeadChip, assembled in the hybridization chamber as instructed by the manufacturer and incubated at 48oC for 16-20 hours.  Following hybridization, the BeadChips were washed and assembled in a fluid flow-through station for primer-extension reaction and staining with reagents and buffers provided.

scan_protocol: Polymer-coated BeadChips were scanned in an iScan scanner (Illumina) using Inf Methylation mode.

data_processing:
Raw IDAT files were processed using R package SeSAMe (PMID: 30085201) with noob background correction (PMID: 23476028, 28035024), non-linear dye bias correction, SNP and non-detection (p-value) masking. Methylation beta values are computed as the fraction of total probeset intensity attributable to fluorescence from the methylated probe allele, with 0 indicating no methylation and 1 indicating full methylation. The SeSAMe/noob default offset of 15 was added to both unmethylated (U) and methylated (M) allelic intensities in each pair to avoid division by zero. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies (PMID: 27924034).
matrix_processed.csv: normalized (SeSAMe) Average Beta
matrix_signals.csv: Unmethylated and methylated signal intensities, and non-detection p-values

source_name: Bone marrow, normal

label_protocol: Bisulfite conversion of genomic DNA was performed with EZ DNA methylation Kit (Zymo Research, Irvine, CA, #D5002) following the manufacturer’s protocol with modifications for the Infinium Methylation Assay. Briefly, 250ng of genomic DNA was mixed with 5 µl of Dilution Buffer and incubated at 37oC for 15 minutes and then mixed with 100 µl of conversion reagent prepared as instructed in the protocol. Mixtures were incubated in a thermocycler for 16 cycles at 95oC for 30 seconds and 50oC for 60 minutes. Bisulfite-converted DNA samples were loaded onto the provided 96-column plates for desulphonation, washing and elution. The concentration of bisulfite-converted, eluted DNA was measured by UV-absorbance using a NanoDrop-1000 (Thermo Fisher Scientific, Waltham, MA).

extract_protocol: Starting with one vial of cryopreserved cells derived from Bone Marrow (or if Bone Marrow unavailable, Peripheral Blood), cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip.

treatment_protocol: Diagnostic (presentation) bone marrow or peripheral blood specimens were collected from patients prior to induction therapy. Additional genomic data types and clinical covariates are available for these specimens under the TARGET-AML study (phs000465), available through the database of genotypes and phenotypes (dbGaP) and the NCI Genomic Data Commons (GDC).

tag: group

value: normal

tag: age at diagnosis (days)


title: WBJPE171125076


title: KLRG1_plus_GFP_plus Replicate 1 [scRNA-seq]


title: KLRG1_plus_GFP_plus Replicate 2 [scRNA-seq]


title: P493_Myc

source_name: P493 Myc


title: WBJPE171125073


title: WBJPE171125075


title: WBJPE171125074


title: P493_Input

source_name: P493 Input


title: gDNA from subject PANXAF

source_name: AML, pre-treatment

value: tumor

value: Male


title: WBJPE171125071


title: WBJPE171125070


title: Treg_Klrg1+GFP+_2 [ATAC-seq]

data_processing:
Sequenced reads were trimmed for adaptor sequences using skewer v0.2.2
Reads were mapped to mm10 whole genome using bowtie2 v2.3.3 with the –very-sensitive parameter and a maximum insert size of 2000 bp
Duplicate and unpaired reads were removed using the sambamba (Tarasov et al., 2015) ‘markdup’ command, and reads with mapping quality >30 and alignment to the nuclear genome were kept.
Peak calling for each sample was performed using HOMER v4.10 (Heinz et al., 2010) with the following approach: Two different peak sets were called, once we used the options ‘-style factor -fragmentLength 150 -size 250 -minDist 250 –L 4 –fdr 0.0001’ parameters, to identify highly robust small regions of open chromatin, and in a second approach we used the parameters ‘-region -fragmentLength 150 -size 150 -minDist 250 -L 4 -fdr 0.0001’ to identify larger regions of open chromatin. The two peak sets were then merged using the mergePeaks function of HOMER to create the peak set that was used for downstream analysis.
For visualization purposes only, coverage files from filtered bam files were produced using bedtools (Quinlan and Hall, 2010) genomeCoverageBed, each position was normalized by dividing to the total library size and multiplying by 106, followed by conversion to a bigwig using the bedGraphToBigWig command from the UCSC genome browser tools.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain bed files (peaks) and bigWig files (for genome browser visuaizations)

extract_protocol: Chromatin accessibility mapping on purified cell populations was performed using the ATAC-seq method as previously described (Buenrostro et al., 2013; Corces et al., 2017), with minor adaptations. Briefly, in each experiment 2,000 - 15,000 sorted cells were pelleted by centrifuging for 10 min at 4 °C at 500 x g. After centrifugation, the pellet was carefully lysed in 50 µl resuspension buffer supplemented with NP-40 (Sigma), Tween-20 and Digitonin (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 % NP-40, 0.1 % Tween-20, 0.01 % Digitonin) and incubated for 3 minutes on ice. Then, 1 ml of ice-cold resuspension buffer supplemented with Tween-20 was added, and the sample was centrifuged at 4 °C at 500 x g for 10 minutes. The supernatant was discarded, and the cell pellet was carefully resuspended in the transposition reaction (25 µl 2 x TD buffer (Illumina), 2.5 µl TDE1 (Illumina), 16.5 µl PBS, 5 µl nuclease-free water, 0.5 µl 1% Digitonin (Promega), 0.5 µl 10% Tween-20 (Sigma)) for 30 min at 37 °C on a shaker at 1000 rpm. Following DNA purification with the Clean and Concentrator-5 kit (Zymo) eluting in 23 µl, 2 µl of the eluted DNA was used in a quantitative 10 µL PCR reaction (1.25 µM forward and reverse custom Nextera primers (Corces et al., 2017), 1x SYBR green final concentration) to estimate the optimum number of amplification cycles with the following program 72°C 5 min; 98°C 30 s; 25 cycles: 98°C 10 s, 63°C 30 s, 72°C 1 min; the final amplification of the library was carried out using the same PCR program and the number of cycles according to the Cq value of the qPCR. Library amplification using custom Nextera primers was followed by SPRI size selection with AmpureXP beads to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). The libraries were sequenced using the Illumina HiSeq 4000 or NextSeq platforms.


title: Treg_Klrg1+GFP+_4 [ATAC-seq]


title: Treg_Klrg1+GFP+_3 [ATAC-seq]


title: WBJPE171125069


title: Treg_Klrg1-GFP+_3 [ATAC-seq]


title: Treg_Klrg1-GFP+_4 [ATAC-seq]


title: WBJPE171125068


title: Treg_Klrg1-GFP+_2 [ATAC-seq]


title: WBJPE171125067


title: WBJPE171125072


title: WBJPE171125066


title: WBJPE171125065


title: WBJPE171125064


title: Treg_Klrg1+GFP+_1 [ATAC-seq]


title: Treg_Klrg1-GFP-_3 [ATAC-seq]


title: Treg_Klrg1-GFP+_1 [ATAC-seq]


title: Treg_Klrg1-GFP-_4 [ATAC-seq]


title: WBJPE171125063


title: GBE HCC Replicate 5

type: RNA

city: Research Triangle Park

first: Deepak

last: Mav

state: NC

address: 2 Davis Drive

institute: Sciome LLC

description: Gene Expression data for GBE HCC Replicate 5

hyb_protocol: 15 µg of amplified biotinylated cDNAs were fragmented and hybridized for 16 hours at 45oC as per Affymetrix protocol

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000, and GeneChip1 Command Console Software (AGCC; Version 1.1) was used to obtain the data. Fluorescent pixel intensity measurements were processed using the MAS5 algorithm (Hubbell, Liu, and Mei 2002), and signals were background subtracted and averaged across probes within a probeset using a mean Tukey biweight function.

data_processing: The CEL files were processed using R, proprocessCore package to compute RMA normalized Signal for each probe set

label: biotin

source_name: GBE HCC 5

label_protocol: Array slides were double stained with streptavidin/phycoerythrin and washed using the EukGE-WS2v5 protocol from the Affymetrix Fluidics Station FS450 for antibody amplification.

growth_protocol: B6C3F1 mouse were used for this study for a period of 2 years.

extract_protocol: RNA were isolated from these selected samples using the Invitrogen PureLink Mini Kit® (Life Technologies Corporation, Carlsbad, CA). RNA quality was assessed using an Agilent Bioanalyzer®. (Agilent Technologies, Inc; Santa Clara, CA).

treatment_protocol: B6C3F1 mouse were either treated with vehicle control or various doses of Ginkgo biloba extract by oral gavage for 2 years as part of National Toxicology Porgram (NTP) Toxicology and Carcinogenesis studies.

tag: cohort

value: GBE HCC

tag: replicate

tag: barcode


title: Treg_Klrg1-GFP-_2 [ATAC-seq]


title: GBE HCC Replicate 4

description: Gene Expression data for GBE HCC Replicate 4

source_name: GBE HCC 4


title: Muscle_N2ICD_rep1

city: Nagasaki

first: Yusuke

last: Ono

address: 1-12-4 Sakamoto

country: Japan

institute: Nagasaki University

description:
N2ICD-mTG
Gene expression in Notch2-activated muscle.

hyb_protocol: 0.6 ug of Cy3-labeled cRNA was fragmented at 60°C for 30 minutes using a Gene Expression Hybridization kit <5188-5242> (Agilent). 0.48 ug of Cy3-labeled cRNA was hybridized to Agilent-028005 SurePrint G3 Mouse GE microarray 8x60K (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, using a Gene Expression Wash Pack <5188-5327> (Agilent), microarrays were washed 1 minute at room temperature with Wash Buffer 1 (Agilent) and 1 minute with 37°C Wash buffer 2 (Agilent), then dried.

scan_protocol: The slide was scanned after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software <version 10.10.1.1> (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities.
Raw fluorescence data was extracted using GeneSpring software 12.6.1 (Agilent). Raw fluorescence values were then subjected to log2 transformation and 75th percentile normalization for analysis.

source_name: tibialis anterior muscle, N2ICD-transgenic

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp labeling kit, one-color <5190-2305> (Agilent), followed by RNeasy mini kit purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from muscle tissues using ISOGEN II (Nippon Gene). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Tibialis anterior muscles were freshly harvested from N2ICD-mTG and control mice.

tag: strain/background

tag: genotype/variation

value: activated Notch2 (N2ICD) transgenic

value: tibialis anterior muscle

tag: age

value: adult


title: GBE HCC Replicate 6

description: Gene Expression data for GBE HCC Replicate 6

source_name: GBE HCC 6


title: Treg_Klrg1-GFP-_1 [ATAC-seq]


title: Muscle_Control_rep1

description:
Control
Gene expression in control muscle.

source_name: tibialis anterior muscle, control

tag: tissue

tag: gender


title: GBE HCC Replicate 1

description: Gene Expression data for GBE HCC Replicate 1

source_name: GBE HCC 1


title: GBE HCC Replicate 3

description: Gene Expression data for GBE HCC Replicate 3

source_name: GBE HCC 3


title: SPNT HCC Replicate 6

description: Gene Expression data for SPNT HCC Replicate 6

source_name: SPNT HCC 6

value: SPNT HCC


title: WBJPE171125062

source_name: skeleton muscle

value: mice skeletal muscle

tag: strain

value: male


title: gDNA from subject PARTYV


title: Skin_Treg_4dup_2 [ATAC-seq]

value: Skin

value: Treg


title: WBJPE171125061


title: gDNA from subject PARPEK


title: GBE HCC Replicate 2

description: Gene Expression data for GBE HCC Replicate 2

source_name: GBE HCC 2


title: SPNT HCC Replicate 5

description: Gene Expression data for SPNT HCC Replicate 5

source_name: SPNT HCC 5


title: WBJPE171125060


title: WBJPE171125059


title: Skin_Treg_3_2 [ATAC-seq]


title: SPNT HCC Replicate 3

description: Gene Expression data for SPNT HCC Replicate 3

source_name: SPNT HCC 3


title: gDNA from subject PATJWN


title: Skin_Treg_2_2 [ATAC-seq]


title: WBJPE171125058


title: Skin_Tconv_4dup_2 [ATAC-seq]

value: Tconv


title: Skin_Tconv_3_2 [ATAC-seq]


title: gDNA from subject PATBHG

value: Female


title: SPNT HCC Replicate 2

description: Gene Expression data for SPNT HCC Replicate 2

source_name: SPNT HCC 2


title: WBJPE171125057


title: gDNA from subject PASHZX


title: Lung_Treg_4 [ATAC-seq]

value: Lung


title: Skin_Tconv_2_2 [ATAC-seq]


title: WBJPE171125055


title: WBJPE171125056


title: WBJPE171125054


title: gDNA from subject PASGEM


title: WBJPE171125053


title: SPNT HCC Replicate 4

description: Gene Expression data for SPNT HCC Replicate 4

source_name: SPNT HCC 4


title: gDNA from subject PATABK


title: SPNT HCC Replicate 1

description: Gene Expression data for SPNT HCC Replicate 1

source_name: SPNT HCC 1


title: Lung_Treg_2 [ATAC-seq]


title: Lung_Treg_3 [ATAC-seq]


title: CNTL Replicate 5

description: Gene Expression data for CNTL Replicate 5

source_name: CNTL 5

value: CNTL


title: CNTL Replicate 4

description: Gene Expression data for CNTL Replicate 4

source_name: CNTL 4


title: CNTL Replicate 2

description: Gene Expression data for CNTL Replicate 2

source_name: CNTL 2


title: Lung_Treg_1 [ATAC-seq]


title: CNTL Replicate 3

description: Gene Expression data for CNTL Replicate 3

source_name: CNTL 3


title: WBJPE171125052


title: CNTL Replicate 6

description: Gene Expression data for CNTL Replicate 6

source_name: CNTL 6


title: CNTL Replicate 1

description: Gene Expression data for CNTL Replicate 1

source_name: CNTL 1


title: gDNA from subject PASCRP

source_name: AML, pre-treatment


title: gDNA from subject PASAXB


title: WBJPE171125051


title: WBJPE171125050


title: gDNA from subject PASFVP


title: Lung_Tconv_4 [ATAC-seq]


title: Lung_Tconv_2 [ATAC-seq]


title: WBJPE171125049


title: Lung_Tconv_3 [ATAC-seq]


title: gDNA from subject PARXVI


title: cell_isolated_E16_rep1

city: Ames

first: Jeff

last: Trimarchi

state: IA

address: 2437 Pammel Drive

department: Genetics, Development and Cell Biology

institute: Iowa State University

description: Gene expression data from a single developing mouse retinal cell

hyb_protocol: Amplified RNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays using standard Affymetrix protocols at either the GeneChip Facility at Iowa State University or the biopolymers facility at Harvard Medical School.

scan_protocol: Affymetrix Mouse Genome 430 2.0 arrays were scanned using standard protocols at either the GeneChip Facility at Iowa State University or Harvard Medical School Biopolymers facility.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

molecule: polyA RNA

source_name: E16 mouse retina

label_protocol: Ten micrograms of each single cell cDNA was digested with DNase I for 13 minutes at 37C, heated to 99C for 15 minutes and biotin labeled using Biotin N6 ddATP (Enzo Biosciences) and TdT (Roche) at 37C for 1.5 hours.

growth_protocol: Retinas were dissected and disocciated with papain at different timepoints. There was no culture or time for growth.

extract_protocol: Individual cmouse retinal cells were harvested using a pulled glass pipette and were expelled into cold lysis buffer. The total single cell RNA was reverse transcribed using Superscript III combined with an oligo dT primer. This first strand cDNA product was tailed with A’s using terminal deoxynucleotidyl transferase (TdT) and PCR amplified for 35 cycles using the same oligo dT primer.

treatment_protocol: Single cells were isolated and immediately placed into cell lysis buffer.

value: dissociated retina

value: expresses Atoh7

tag: developmental stage


title: cell_isolated_E14_rep7

source_name: E14 mouse retina


title: gDNA from subject PARXDI

value: tumor


title: WBJPE171125048


title: Lung_Tconv_1 [ATAC-seq]

tag: cell type


title: cell_isolated_E14_rep4


title: WBJPE171125047


title: LN_Naive_Treg_4 [ATAC-seq]


title: gDNA from subject PARVXT


title: gDNA from subject PARVLP

value: Male


title: gDNA from subject PARLHW


title: WBJPE171125046


title: WBJPE171125044


title: LN_Naive_Treg_1 [ATAC-seq]


title: LN_Naive_Treg_3 [ATAC-seq]


title: LN_Mem_Treg_4 [ATAC-seq]


title: WBJPE171125043


title: WBJPE171125042


title: WBJPE171125041


title: cell_isolated_E14_rep6


title: LN_Naive_Treg_2 [ATAC-seq]


title: gDNA from subject PARIYB


title: gDNA from subject PARHKY


title: WBJPE171125040


title: gDNA from subject PARJLW


title: cell_isolated_E14_rep2


title: cell_isolated_E14_rep3


title: gDNA from subject PARFWM


title: gDNA from subject PASZZE


title: cell_isolated_E14_rep5


title: WBJPE171125039


title: cell_isolated_E14_rep1


title: LN_Mem_Treg_1 [ATAC-seq]


title: LN_Mem_Treg_2 [ATAC-seq]


title: gDNA from subject PARFKS


title: LN_Mem_Treg_3 [ATAC-seq]


title: Fat_Treg_3 [ATAC-seq]

value: Fat

value: TconvTreg


title: cell_isolated_E12_rep2

source_name: E12 mouse retina


title: WBJPE171125037

source_name: skeleton muscle


title: cell_isolated_E12_rep1


title: gDNA from subject PARFLB


title: Fat_Treg_2 [ATAC-seq]


title: Jmjd2c depleted cells at day 3, biological rep1

city: Taipei

first: Kuo-Hsuan

last: Hung

address: 128 Academia Road, Section 2

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description:
D3-2C-1
Gene expression data from Jmjd2c depleted cells at Day 3

hyb_protocol: Approximately 2 μg of RNA was labeled and hybridized to GeneChip Mouse Genome 430 2.0 arrays (Affymetrix) according to the manufacturer's protocols, and GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000-7g.

data_processing: All data analysis was performed using GeneSpring software GX 7.3.1 (Agilent Technologies)

source_name: mouse B220+ B cells treated with Tfh-derived signals along with shJmjd2c virus

label_protocol: biotininated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: B220+ B cells are purified by MACS beads (Miltenyi Biotec), cultured in RPMI medium with 10% FBS

extract_protocol: Total RNA from 107 stimulated mouse B220+ B cells was extracted with TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions.

treatment_protocol: B220+ B cells are stimulated with anti-CD40, IL21, and HEL, along with transfection of sicontrol, siJmjd2a or siJmjd2c ,for 1 day or 3 days

tag: transgene

tag: organ

value: spleen


title: Jmjd2c depleted cells at day 3, biological rep2

description:
D3-2C-2
Gene expression data from Jmjd2c depleted cells at Day 3


title: gDNA from subject PARAFA


title: cell_isolated_E13_rep1

source_name: E13 mouse retina


title: WBJPE171125036


title: Fat_Treg_1 [ATAC-seq]


title: gDNA from subject PASURM


title: WBJPE171125038


title: WBJPE171125034


title: WBJPE171125035


title: gDNA from subject PASRIN


title: Jmjd2a depleted cells at day 3, biological rep2

description:
D3-2A-2
Gene expression data from Jmjd2a depleted cells at Day 3

source_name: mouse B220+ B cells treated with Tfh-derived signals along with shJmjd2a virus


title: gDNA from subject PASKDS


title: Fat_Tconv_3 [ATAC-seq]

value: TconvTconv


title: Fat_Tconv_2 [ATAC-seq]


title: WBJPE171125033


title: WBJPE171125032


title: Jmjd2a depleted cells at day 3, biological rep1

description:
D3-2A-1
Gene expression data from Jmjd2a depleted cells at Day 3


title: control group at day 3, biological rep1

description:
D3-Ct-1
Gene expression data from control group at Day 3

source_name: mouse B220+ B cells treated with Tfh-derived signals along with shcontrol virus


title: control group at day 3, biological rep2


title: gDNA from subject PASJYX


title: WBJPE171125031


title: Fat_Tconv_1 [ATAC-seq]


title: Colon_Treg_4 [ATAC-seq]

value: Colon


title: gDNA from subject PASJCL


title: Fat_Tconv_4 [ATAC-seq]


title: Colon_Treg_3 [ATAC-seq]


title: WBJPE171125030

value: mice skeletal muscle


title: Jmjd2c depleted cells at day 1, biological rep1

description:
D1-2C-1
Gene expression data from Jmjd2c depleted cells at Day 1


title: Jmjd2c depleted cells at day 1, biological rep2

description:
D1-2C-2
Gene expression data from Jmjd2c depleted cells at Day 1


title: Jmjd2a depleted cells at day 1, biological rep2

description:
D1-2A-2
Gene expression data from Jmjd2a depleted cells at Day 1


title: gDNA from subject PATHAE


title: gDNA from subject PASDUD


title: control group at day 1, biological rep2

description:
D1-Ct-2
Gene expression data from control group at Day 1


title: Colon_Treg_1 [ATAC-seq]


title: Colon_Tconv_4 [ATAC-seq]


title: WBJPE171125029

value: male


title: control group at day 1, biological rep1

description:
D1-Ct-1
Gene expression data from control group at Day 1


title: Jmjd2a depleted cells at day 1, biological rep1

description:
D1-2A-1
Gene expression data from Jmjd2a depleted cells at Day 1


title: Colon_Tconv_3 [ATAC-seq]


title: Plasma_IMB_BiolRep3

city: Prague 10

first: Veronika

last: Boušková

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

description: miRNA expression

hyb_protocol: The Cy3-labeled samples were hybridized for 20 h at 55 °C in a rotator oven. The washing steps were proceed according to the manufactures’  instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan microarray scanner using AgilentG3_miRNA protocol (Scan Area 61 × 21.6 mm, Scan resolution 3 μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1  (Agilent) using default parameters (Grid: 070155) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Plasma, 3 mice, IMB_9×100mg/kg, 9days, BiolRep3

label_protocol: 3.1 µl of isolated total RNA was labeled with Cy3 using the miRNA Complete Labeling and Hybridization Kit (Agilent Technologies).

growth_protocol: Female NMRI mice, 3-month old, weighing 30-33g

extract_protocol: Total RNA was isolated from 300 μl of plasma (pooled sample of 3 treated mice as a biological replicate) by miRNeasy Serum/Plasma Kit (Qiagen) according to manufactures’ protocol.

treatment_protocol: Mice were randomly divided in three groups. The animals in the first group  (n=9) were treated p.o. with IMB (distilled water solution) in daily dose 100 mg/kg of body weight for 9 consecutive days. The animals in the second group (n=9) were treated i.v. (tail vein) with DOX in saline solution (one dose 3mg/kg, 4 doses, application every other day). The mice in control group (n=6) were treated with the solvents only.

value: plasma

value: female

value: NMRI

value: 3 months


title: gDNA from subject PASJZX


title: gDNA from subject PASMRU


title: WBJPE171125026


title: Plasma_DOX_BiolRep3

description: miRNA expression

source_name: Plasma, 3 mice, DOX_4×3mg/kg, 9days, BiolRep3


title: Plasma_CTRL_BiolRep2

description: miRNA expression

source_name: Plasma, 3 mice, solvents only, 9days, BiolRep2


title: MLL1-induced rep 3

city: Aurora

first: Patricia

last: Ernst

state: CO

department: Pediatrics

institute: University of Colorado

data_processing:
Base calling and quality scoring was performed using Illumina Real-Time Analysis (RTA) v2.7.3 software
Files were demultiplexed and converted from bcl to fastq format using bcl2fastq2 Conversion v2.16.0.10 software
Reads were trimmed using Trimmomatic v0.36
Reads were mapped to mm10 using GMAP/GSNAP v20141217
FPKM values were derived using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: Cufflinks tab-delimited output files containing FPKM values for each sample

source_name: hMLL1 clone 18 treated with doxycycline

growth_protocol: ES clones were differentiated as suspension EBs for 6 days total with doxycycline at 1 µg/mL present from day 4-day 6

extract_protocol:
Total RNA was extracted with Qiagen Rneasy Mini Kit
Libraries were prepared using the Nugen-mRNA mouse library prep kit
RNA High throughput sequencing using an Illumina HiSeq 4000

treatment_protocol: At day 6, cells were dissociated with collagenase and dispase, incubated with c-Kit and CD41 antibodies and viable c-Kit/CD41 double positive cells sorted

tag: cell line background

value: hMLL1 clone 18; doxycycline-inducible MLL1 transgene

tag: treatment

value: day 4-6 doxycycline

value: c-Kit+/CD41+ hematopoietic progenitors


title: MLL1-induced rep 2


title: gDNA from subject PARIEG

tag: group

value: Female


title: WBJPE171125025


title: WBJPE171125023


title: MLL1-induced rep 1


title: WBJPE171125027


title: Plasma_DOX_BiolRep2

description: miRNA expression

source_name: Plasma, 3 mice, DOX_4×3mg/kg, 9days, BiolRep2


title: Plasma_IMB_BiolRep2

description: miRNA expression

source_name: Plasma, 3 mice, IMB_9×100mg/kg, 9days, BiolRep2


title: Plasma_CTRL_BiolRep1

description: miRNA expression

source_name: Plasma, 3 mice, solvents only, 9days, BiolRep1


title: KH2 control rep 2

source_name: KH2 treated with doxycycline

value: control


title: WBJPE171125020


title: KH2 control rep 1


title: SU5402_late_9h_1

city: BANYULS SUR MER

first: Stephanie

last: Bertrand

address: AVENUE PIERRE FABRE

country: France

institute: CNRS/SU UMR7232

description: SU5402 50µM

data_processing:
The first 50 bases of pass-filter reads were retained, in order to be comparable between the different samples.
These reads were mapped onto the reference transcriptome (https://wwwphp.obs-banyuls.fr/repository/transcriptome_B_lanceolatum/TotalMergeAssembliesGenbankRenomme.fasta.gz) using bwa v0.6.1 29 and the following set of parameters : -l 27 -n 4 -e 4. Only uniquely aligned reads were then retained. The number of reads aligned to each contig was computed using R.
Genome_build: Reference transcriptome constructed using data from Oulion et al (PLoS One. 2012; 7(5): e36554) and the data obtained in this study, available on the following URL : https://wwwphp.obs-banyuls.fr/repository/transcriptome_B_lanceolatum/TotalMergeAssembliesGenbankRenomme.fasta.gz
Supplementary_files_format_and_content: Tabulated text file containing raw read counts in each sample.

organism: Branchiostoma lanceolatum

source_name: Mix of whole embryos

growth_protocol: Embryos were grown in 6cm Petri dishes filled with 6mL of filtered sea water with DMSO or SU5402.

extract_protocol:
Embryos were frozen in liquid nitrogen after getting rid of the filtered sea water by centrifugation. Total RNA was extracted using the RNeasy Mini Plus Kit from QIAGEN following manufacturer's instructions. Disruption and homogenization were undertaken using TissueLyzer from QIAGEN.
A library of template molecules suitable for high throughput DNA sequencing was created following the Illumina “Truseq RNA sample preparation low throughput” protocol with some modifications. Briefly, mRNA was purified from 2 µg total RNA using oligo-dT magnetic beads and fragmented using divalent cations at 94°C for 8 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers, then the second strand of the cDNA was synthesized using Polymerase I and RNase H. The next steps of RNA-Seq library preparation were performed in an automated system using SPRIworks Fragment Library System I kit (ref A84801, Beckman Coulter, Inc) with the SPRI-TE instrument (Beckman Coulter, Inc). Briefly, in this system double stranded cDNA fragments were blunted, phosphorylated and ligated to indexed adapter dimers, and fragments in the range of ~200-400 bp were size selected. The automated steps were followed by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 15 cycles (6 hpt libraries) or 12 cycles (3 and 9 hpt libraries); 5 min at 72°C), then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent).

treatment_protocol: Embryos were treated with 0,1% DMSO or 50µM SU5402.

value: SU5402 50microM

tag: time of treatment


title: SU5402_late_9h_2

description: SU5402 50µM


title: WBJPE171125021


title: gDNA from subject PATLXB

source_name: AML, pre-treatment

value: tumor

tag: age at diagnosis (days)


title: KH2 control rep 3


title: Ctrl_Young_HeartEC_182

city: New York City

first: Balvir

last: Kunar

state: New York

address: 1300 York Ave

department: Regenerative Medicine; Physiology, Biophysics, & Systems Biology

institute: Weill Cornell Medical College

data_processing:
Base calling and sequencing reads de-multiplexing were performed using bcl2fastq v2.17.
Sequencing reads were checked for quality (FastQC v0.11.5), and trimmed/filtered using Trimmomatic v0.36.
Read alignment to the transcriptome sequence reference of the UCSC mm10 genome build were performed using TopHat2 v2.1.0.
Mapped reads were assembled into transcripts, and abundance measures (FPKM values) quantified using Cufflinks v2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: Single tab-delimited data-matrix with GENE_ID, GENE_DESCRIPTION, and SAMPLE_NAMES. All numerical inputs represent FPKM values.

extract_protocol:
At least 100 ng of total RNA from both freshly harvested and cultured cells was isolated (phenol-chloroform separation of TRIzol LS) and purified using Qiagen’s RNeasy Mini Kit.
RNA library preps were prepared and multiplexed using Illumina’s TruSeq RNA Library Preparation Kit v2 (non-stranded and poly-A selection) and 10 nM of cDNA was used as input for high-throughput sequencing via Illumina’s HiSeq 4000 producing 51 bp paired-end reads.

treatment_protocol: All cell populations were purified via FACS. Purity mask was applied.

tag: strain background

tag: tissue source

value: heart

value: endothelial cell

value: wild type

tag: co-culture status

value: freshly isolated from tissue


title: Plasma_IMB_BiolRep1

description: miRNA expression

source_name: Plasma, 3 mice, IMB_9×100mg/kg, 9days, BiolRep1


title: Plasma_DOX_BiolRep1

description: miRNA expression

source_name: Plasma, 3 mice, DOX_4×3mg/kg, 9days, BiolRep1


title: gDNA from subject PATLJF


title: WBJPE171125024

source_name: skeleton muscle

value: mice skeletal muscle


title: Ctrl_late_9h_2

description: DMSO 0.1%

value: DMSO 0.1percent


title: Colon_Tconv_1 [ATAC-seq]

value: Colon

value: Tconv


title: WBJPE171125022

value: male


title: Ctrl_late_9h_1

description: DMSO 0.1%


title: Ctrl_Young_HeartEC_178

tag: genotype/variation


title: ECp53KO_Young_HeartEC_172


title: SU5402_late_3h_2

description: SU5402 50µM


title: gDNA from subject PATCVL

value: Male


title: ECp53KO_Young_HeartEC_170


title: WBJPE171125015


title: SU5402_late_3h_1

description: SU5402 50µM


title: gDNA from subject PATCBV


title: Ctrl_late_3h_2

description: DMSO 0.1%


title: gDNA from subject PASXNT


title: AMG-treated 5h - replicate 4

city: Leuven

first: Frederic

last: Lluis

state: Leuven

address: Herestraat 49

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

description:
GC059138
Normalized_counts_replicate_2_3_4.csv

data_processing:
50 bp single-end reads were generated. An average of 20 million reads were obtained from all samples. Quality control of raw reads was performed with the FastQC v0.11.5. The adapters were filtered with ea-utils v1.2.2.18. The splice-aware alignment was performed with TopHat v2.0.13 against the mouse genome mm10. The number of allowed mismatches was 2. Reads that mapped to more than one site to the reference genome were discarded.  The minimal score of alignment quality to be included in count analysis was 10. Resulting SAM and BAM alignment files were handled with Samtools v0.1.19.24. Quantification of reads per gene was performed with HT-Seq count v0.5.3p3. Count-based differential expression analysis was done with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor package DESeq. Reported p-values were adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR).
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing matrix with read counts normalized by the library size for all samples

source_name: Primary fibroblasts

growth_protocol: Mouse primary fibroblasts were isolated from the end of the tail (0,5 cm) of C57BL/6 mouse model under anesthesia (isoflurane). Tails were disaggregated by collagenase IV digestion for 40 minutes at 37°C in agitation. The obtained cells were cultured in DMEM GlutaMax (Ca No. 61965-026, Gibco Life Science, Grand island) supplemented with 10% of fetal bovine serum, 1% of penicillin-streptomycin, 1% of L-glutamine, 1% of sodium pyruvate and 1% of nonessential amino acids at 37°C in a humidified incubator with 5% of CO2

extract_protocol:
Autologous micrografts (AMG) were obtained from skin murine biopsies (1 cm2) using a sterile tissue destroyer (Rigeneracons). Tissues were re-suspended in 1 mL PBS, disrupted, and filtered through 70 m filter membranes.
Library preparation was performed with the Illumina TruSeq Stranded mRNA Sample Preparation Kit, according to the manufacturers protocol (48 samples, Cat No. 20020594). Denaturation of RNA was performed at 65oC in a thermocycler and cooled down to 4oC. Samples were indexed to allow for multiplexing. Sequencing libraries were quantified using the Qubit fluorometer (Thermo Fisher Scientific, Massachusetts, USA). Library quality and size range was assessed using the Bioanalyzer (Agilent Technologies) with the DNA 1000 kit (Agilent Technologies, California, USA) according to the manufacturer’s instructions. Libraries were diluted to a final concentration of 2nM and sequenced on Illumina HiSeq4000 sequencing system, according to the manufacturer’s recommendations.

treatment_protocol: The extracted AMG were then diluted 1:10 in growth media and applied on murine primary fibroblasts on an in vitro model of wound healing (cell scratch assay)

value: AMG-treated

tag: time

value: 5h hours


title: gDNA from subject PATGTL


title: Ctrl_late_3h_1

description: DMSO 0.1%


title: WBJPE171125014

tag: tissue


title: AMG-treated 5h - replicate 3

description:
GC059137
Normalized_counts_replicate_2_3_4.csv


title: WBJPE171125012

tag: gender


title: WBJPE171125018

tag: strain


title: SU5402_early_9h_1

description: SU5402 50µM

tag: developmental stage


title: SU5402_early_9h_2

description: SU5402 50µM


title: WBJPE171125019


title: WBJPE171125017


title: Untreated 5h - replicate 4

description:
GC059135
Normalized_counts_replicate_2_3_4.csv

value: Untreated


title: Ctrl_early_9h_2

description: DMSO 0.1%


title: gDNA from subject PASFFS


title: WBJPE171125010


title: WBJPE171125016


title: gDNA from subject PARUZS

value: Female


title: Ctrl_early_9h_1

description: DMSO 0.1%


title: gDNA from subject PARUEX


title: WBJPE171125009


title: WBJPE171125008


title: SU5402_early_3h_2

description: SU5402 50µM


title: gDNA from subject PARNFZ


title: Untreated 24h - replicate 1

description:
GC043251
Normalized_counts_replicate1.csv

value: 24 hours


title: WBJPE171125013


title: AMG-treated 5h - replicate 2

description:
GC059136
Normalized_counts_replicate_2_3_4.csv


title: WBJPE171125006


title: gDNA from subject PARMST


title: Ctrl_early_3h_2

description: DMSO 0.1%


title: WBJPE171125011


title: WBJPE171125005


title: gDNA from subject PARKUY


title: Untreated 12h - replicate 1

description:
GC043247
Normalized_counts_replicate1.csv

value: 12 hours


title: Untreated 5h - replicate 3

description:
GC059134
Normalized_counts_replicate_2_3_4.csv


title: Untreated 5h - replicate 2

description:
GC059133
Normalized_counts_replicate_2_3_4.csv


title: gDNA from subject PARHUP

value: tumor


title: AMG-treated 24h - replicate 1

description:
GC043253
Normalized_counts_replicate1.csv


title: AMG-treated 5h - replicate 1

description:
GC043245
Normalized_counts_replicate1.csv

value: 5 hours


title: WBJPE171125004


title: WBJPE171125007


title: Untreated 5h - replicate 1

description:
GC043243
Normalized_counts_replicate1.csv


title: gDNA from subject PARFVC


title: mRNA_Si-TINCR-2 rep3

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Bowtie2 is used to map clean reads to the reference genome Homo sapiens GRCh38.p12 . Bowtie2 : -q -L 16 --phred64 -p 6
RSEM was used to calculate gene expression levels of each sample. Default parameters was used.
Genome_build: Homo sapiens GRCh38.p12
Supplementary_files_format_and_content: csv files include RPKM values for each Sample

growth_protocol: Human breast cancer cell lines UACC-812 was obtained from the Chinese Academy of Sciences Cell Bank and Cellbio (China) and cultured and stored according to their instructions.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human breast cancer cell lines UACC-812 was seeded in 6-well dishes the night before to give 60-70% confluence for plasmid and 40-50% for miRNA or siRNA transfection. Cells were transfected using Lipofectamine 2000 (invitrogen), according to the manufacturer’s instructions in the following day. At 48 h post-transfection, cells were harvested for qRT-PCR analysis.

tag: cell type

value: breast cancer cell line

tag: knockdown

value: TINCR


title: SU5402_early_3h_1

description: SU5402 50µM

value: SU5402 50microM


title: Ctrl_early_3h_1

description: DMSO 0.1%


title: mRNA_Si-TINCR-2 rep2


title: mRNA_Si-TINCR-2 rep1


title: AMG-treated 1h - replicate 1

description:
GC043241
Normalized_counts_replicate1.csv

value: 1 hour


title: gDNA from subject PARFMY


title: WBJPE171125002

data_processing:
Illumina Casava1.7 software used for basecalling.
Single-cell RNA sequence reads were evaluated by FastQC
Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than 20.
The reads were mapped to the mm9 using bowtie2.
The mapped reads for genes were counted via Htseq.

extract_protocol:
Cells were isolated by preplating mehods (Nat. Protocols 3, 1501-1509 (2008)).
single cell were captured, lysated, preamplified and library prepared according to "Using the C1 High-Throughput IFC to Generate Single-Cell cDNA Libraries for mRNA Sequencing"

value: mice skeletal muscle


title: mRNA_Si-TINCR-1 rep3


title: AMG-treated 12h - replicate 1

description:
GC043249
Normalized_counts_replicate1.csv


title: Untreated 1h - replicate 1

description:
GC043239
Normalized_counts_replicate1.csv


title: gDNA from subject PAREHK


title: WBJPE171125001


title: mRNA_Si-TINCR-1 rep2


title: HFD Knockout Rep. 2 (Nr5a2 fl;AAV8-Cre)

city: San Francisco

first: Diego

last: Miranda

state: CA

address: 1550 4th Street

department: Cellular and Molecular Pharmacology

institute: Ucsf

description: Cre 819

data_processing:
Samples were sequenced and demultiplexed by the UCSF Center for Advanced Technology.
Sequenced reads were mapped to mm9 whole genome using TopHat v2.1.0.
Reads that aligned to exons were quantified using htseq-count and the mm9 gene model.
Differential gene expression was determined using DESeq2 v1.14.1.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *_htseq_count.txt: Tab-delimited text files include number of exon-aligned reads for the given genes.

source_name: Liver, HFD

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Nugen Ovation RNA-Seq System V2 Sample Prep Kit (Cat#7102) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using manufacturer's protocol.

treatment_protocol: Mice were fed a standard diet (SD) or a high-fat diet (HFD) for 6 weeks.

tag: strain/background

value: Mixed Background 129SvEV-C57BL/6

value: Cre

tag: diet

value: 6 Weeks High Fat (D12492)

tag: age

value: 14 weeks

tag: Sex

value: Liver


title: HFD Knockout Rep. 1 (Nr5a2 fl;AAV8-Cre)

description: Cre 816

value: Male


title: mRNA_NC rep3

value: scramble


title: mRNA_Si-TINCR-1 rep1


title: HFD Control Rep. 4 (Nr5a2 fl)

description: F/F 851

value: F/F


title: mNXF1_RSLP

city: Rochester

first: jinlong

last: lu

address: 213 Hutchinson Hall

institute: University of Rochester

description: processed data file: mutRSLP_reads count.txt

data_processing:
Basecalls performed using CASAVA version
RSLP library sequencing reads were aligned to the mm9 genome assembly using Bowtie version 1.0.0 with the default parameters
RSLP library sequencing reads reads were aligned to the mm9 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
Reads density of RSLP targeted regions were calculated through bedtools intersect, identify the overlapped reads of mapped reads and targeted regions, 10 bp of each bin
Fold changes of chromatin fraction and cytoplasmic fraction were calculated through normalized reads density from cytopasmic fraction by chromatin fraction
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include fold changes and p values of RSLP samples, and reads count of different mutations of mNxf1 sample

source_name: 46C mES cells

growth_protocol: ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold12 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification k
RNA-Seq of RSLP targeted regions

treatment_protocol: Cells were washed once with cold PBS, and then add TRIzol for RNA total RNA extraction

value: embryonic stem cells

tag: treatment

value: transfected with RSLP library


title: mRNA_NC rep2


title: WBJPE171125003

city: Hangzhou

first: Yixiao

last: Liu

institute: Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine

value: male


title: GFP-RTM-46C

description: processed data file: RTM samples_reads density comparison.txt

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold 9 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification k
RNA-Seq of RSLP targeted regions


title: 5AI-RTM-short-2

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold 6 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification k
RNA-Seq of RSLP targeted regions


title: HFD Control Rep. 3 (Nr5a2 fl)

description: F/F 843


title: gDNA from subject PASUUD

extract_protocol: Starting with one vial of cryopreserved cells derived from Bone Marrow (or if Bone Marrow unavailable, Peripheral Blood), cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip.

tag: group

value: tumor

tag: age at diagnosis (days)


title: gDNA from subject PASTZU


title: 5AI-RTM-short-1

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold 5 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification k
RNA-Seq of RSLP targeted regions


title: gDNA from subject PASNRB

value: Female


title: HFD Control Rep. 2 (Nr5a2 fl)

description: F/F 841


title: GFP-Xist-293T

description: processed data file: Xist samples_reads density comparison.txt

source_name: HEK 293T

growth_protocol: 293T cells  were maintained in medium supplemented with 10% heat-inactivated FCS, Penicillin-Streptomycin Solution (100 × stock, Life Technologies).

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold10 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification k
RNA-Seq of RSLP targeted regions

value: Human Embryonic Kidney Cells


title: GFP-RTM-293T

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold 8 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification k
RNA-Seq of RSLP targeted regions


title: HFD Control Rep. 1 (Nr5a2 fl)

description: F/F 829


title: Knockout Rep. 3 (Nr5a2 fl;AAV8-Cre)

description: Cre 14

source_name: Liver, SD

value: Standard


title: gDNA from subject PASKNV


title: Control Replicate 3

city: Philadelphia

first: Joshua

middle: P

last: Earl

state: PA

department: Microbiology and Immunology

institute: Drexel University College of Medicine

description: Control Replicate 3

data_processing:
Raw Nextseq data quality checked and filtered
Hisat2 alignments to E. coli C reference
Stringtie counts of gene features
Deseq2 Analysis of differential abundance
Genome_build: ASM207922v1
Supplementary_files_format_and_content: Stringtie results, diff_exp_genes_padj.tsv

organism: Escherichia coli

source_name: Control Replicate 3

growth_protocol: Total RNA was extracted from a five days old slide biofilms which were transferred to a fresh LB Miller broth daily. As planktonic cells we used cells detached from the biofilm from the last, 5th day passage.

extract_protocol:
Extracted RNAs were processed with Illumina’s Ribozero bacteria kit to deplete of rRNA
Illumina’s TruSeq stranded RNA LT kit was used for Library construction.
Samples were run on 1x75 chip on Illumina Nextseq 500 machine.

treatment_protocol: Planktonic (control) or biofilm (experiment)

tag: experimental condition

value: control


title: 5AI-Xist-293T

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold 7 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification k
RNA-Seq of RSLP targeted regions


title: Knockout Rep. 2 (Nr5a2 fl;AAV8-Cre)

description: Cre 13


title: Control Replicate 2

description: Control Replicate 2

source_name: Control Replicate 2


title: 3AI-Xist-46C

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold 3 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification k
RNA-Seq of RSLP targeted regions


title: 5AI-RTM-293T

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold 4 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification k
RNA-Seq of RSLP targeted regions


title: GFP-Xist-46C

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold11 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification k
RNA-Seq of RSLP targeted regions


title: Control Replicate 1

description: Control Replicate 1

source_name: Control Replicate 1


title: 3AI-Xist-293T

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold 2 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification k
RNA-Seq of RSLP targeted regions


title: Control Rep. 3 (Nr5a2 fl)

description: F/F 6


title: mRNA_NC rep1

value: breast cancer cell line


title: Knockout Rep. 1 (Nr5a2 fl;AAV8-Cre)

description: Cre 11

value: Mixed Background 129SvEV-C57BL/6


title: Control Rep. 2 (Nr5a2 fl)

description: F/F 5


title: 3AI-RTM-293T

extract_protocol:
Cells were harvested at 24 hours after plating. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
RNAs were treated with DNase I for 20 minutes to remove the residue DNA, and reverse-transcribed with SuperScript III Reverse Transcriptase (ThermoFisher). Sequence specific RT primer that targeting the downstream of insertion site of RSLP library was used for the reverse-transcription. The reverse-transcription was performed at 50℃ for 40 minutes and 55℃ for another 20 minutes. 10 U exonuclease I was added and incubate at 37℃ for 20 minute to remove the free RT primers. The reaction was stopped by boil the sample at 95℃ for 10 minutes to inactivate all the enzymes. 0.5 ul 10 mg/ml RNase A was added and incubate at 37℃ for 20 minutes to degrade the RNA. Ethanol precipitation and downstream wash steps were performed as described before. The purified cDNAs were then used as templates for PCR and library construction. Library was prepared by NEBNext Ultra II DNA library preparation kit according to the standard protocols provided by the manufacturer.
RNA-Seq of RSLP targeted regions


title: gDNA from subject PATMIY


title: Biofilm Replicate 2

description: Biofilm Replicate 2

source_name: Biofilm Replicate 2

value: biofilm


title: Biofilm Replicate 3

description: Biofilm Replicate 3

source_name: Biofilm Replicate 3


title: gDNA from subject PASECW


title: S5_4

city: Copenhagen

first: Rasmus

last: Hartmann-Petersen

address: Ole Maaloes Vej 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

data_processing:
Samples were sequenced on a Illumina HiSeq 2000 machine, basecalled and demultiplexed by BGI.
Sequenced reads were aligned to the S.pombe genome (BioProject ID: PRJNA13836; 27-FEB-2015) using bwa mem (v0.7.12) with default settings giving an alignment rate >98% for all samples.
Mapped reads were assigned to GenBank genes (BioProject ID: PRJNA13836; 27-FEB-2015) using GFOLD (’gfold count’)
Genome_build: S.pombe 0.7.12-r1039
Supplementary_files_format_and_content: Count files (.cnt.txt) has five columns: GeneID, GeneSymbol, raw count, total exon length, RPKM

organism: Schizosaccharomyces pombe

source_name: S. pombe_S5

growth_protocol: Wild type S. pombe cells carrying no selection markers were cultured in YES (5 g/L yeast extract, 30 g/L glucose, 225 mg/L adenine, 225 mg/L uracil, 225 mg/L leucine) until exponential phase.

extract_protocol: The cells were harvested by centrifugation (5000 g, 10 min) and total RNA was purified using hot phenol as described in PMID: 12854975.

treatment_protocol: The cells were either untreated (S0_1;S0_2;S0_3;S0_4), or incubated in YES with 100% D2O for 5 hours (S5_1;S5_2;S5_3;S5_4), or incubated in YES with 100% D2O for 24 hours (S24_1;S24_2;S24_3;S24_4).

value: wild type

tag: growth phase

value: exponential phase

tag: growth condition

value: 5 hours in YES (D2O)


title: gDNA from subject PARWPW

data_processing:
Raw IDAT files were processed using R package SeSAMe (PMID: 30085201) with noob background correction (PMID: 23476028, 28035024), non-linear dye bias correction, SNP and non-detection (p-value) masking. Methylation beta values are computed as the fraction of total probeset intensity attributable to fluorescence from the methylated probe allele, with 0 indicating no methylation and 1 indicating full methylation. The SeSAMe/noob default offset of 15 was added to both unmethylated (U) and methylated (M) allelic intensities in each pair to avoid division by zero. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies (PMID: 27924034).
matrix_processed.csv: normalized (SeSAMe) Average Beta
matrix_signals.csv: Unmethylated and methylated signal intensities, and non-detection p-values

value: Male


title: Control Rep. 1 (Nr5a2 fl)

description: F/F 8

tag: genotype/variation

value: 14 weeks

value: Liver


title: Biofilm Replicate 1

description: Biofilm Replicate 1

source_name: Biofilm Replicate 1


title: MCF10CA1a_R1 OE_1

city: Burlington

first: Nicholas

middle: H

last: Farina

state: VT

address: 89 Beaumont Avenue

department: Biochemistry

institute: University of Vermont Cancer Center

hyb_protocol: Total RNAs from cell lines (500 ng) were hybridized on our custom tsRNA microarray chips by following standard protocols. In particular, for the custom tsRNA microarray chips we used a Tecan HS4800 hybridization station, and images were analyzed by using GenePix Pro Software (Molecular Devices).

data_processing: Custom tsRNA microarray data were analyzed by applying normexp negative background correction and quantile data normalization using the Linear Models for Microarray Data (LIMMA) package  from the Bioconductor R project. Differential expression analysis and one-way ANOVA performed in SpotFire DecisionSite v2 (TIBCO).

source_name: Cell line

growth_protocol: Cell line dependant

extract_protocol: TRIzol and sodium acetate RNA precipitation

treatment_protocol: Cell line dependant

tag: cell line

value: RUNX1 Overexpression


title: gDNA from subject PASJDV

city: Little Rock

first: Jason

last: Farrar

institute: University of Arkansas for Medical Sciences

source_name: AML, pre-treatment

tag: gender


title: S5_3


title: gDNA from subject PASGWH


title: MCF10CA1a_R1 OE_2

scan_protocol: Total RNAs from cell lines (500 ng) were hybridized on our custom tsRNA microarray chips by following standard protocols. In particular, for the custom tsRNA microarray chips we used a Tecan HS4800 hybridization station, and images were analyzed by using GenePix Pro Software (Molecular Devices).


title: MCF10CA1a_R1 OE_3

label_protocol: Total RNAs from cell lines (500 ng) were hybridized on our custom tsRNA microarray chips by following standard protocols. In particular, for the custom tsRNA microarray chips we used a Tecan HS4800 hybridization station, and images were analyzed by using GenePix Pro Software (Molecular Devices).


title: S5_1


title: S5_2


title: gDNA from subject PARYGA


title: MCF10CA1a_EV_3

value: Empty Vector


title: S24_4

source_name: S. pombe_S24

value: 24 hours in YES (D2O)


title: S24_3


title: MCF10CA1a_EV_1


title: S24_2


title: MCF10A_shR1-C4_3

value: shRNA against RUNX1


title: S24_1


title: miRXploreUR_rep2

city: Cambridge

first: Jennifer

last: Hu

address: 77 Massachusetts Ave

institute: MIT

description:
Sample 17
synthetic oligos based on miRNA sequences
RNA (synthetic, not extracted)
180719_GEO_miRNAs.txt

data_processing:
Processing pipeline 2: Raw reads were trimmed using tastxtoolkit/0.013. A minimum adapter alignment length of 10bp was required, and unknown (N) nucleotides were kept. The number of exact sequencing read matches to the reference miRNA sequences was tabulated.
Library strategy: AQRNA-seq
Genome_build: RNA Oligo standards, miRXplore Universal Reference
Supplementary_files_format_and_content: Tab-delimited text files containing  the names of target RNA species and their associated read counts

organism: synthetic construct

source_name: synthetic oligos based on human, mouse, viral miRNA sequences

extract_protocol:
The samples used here are synthesized single-stranded RNA oligos. In the case of the oligo mixtures, each sample contained mixtures of 5 oligos of differing lengths and at different concentrations. The miRXplore Universal Reference sample was used as is according to manufacturer's directions.
The RNA oligos were dephosphorylated in a 5 μl reaction containing 0.5 μl of reaction buffer (NEB T4 RNA ligase buffer) and 1 U of shrimp alkaline phosphatase (rSAP, NEB) at 37 °C for 30 min. The reaction was stopped by heat inactivation at 65 °C for 5 min followed by cooling on ice. Linker 1 ligation was performed by adding the following reagents directly to the dephosphorylation product: 1 μl Linker 1 (100 pmol/ul), 3 μl ATP (10 mM, NEB), 2.5 μl T4 RNA ligase buffer (NEB), 2 μl T4 RNA ligase 1 (30U/ul, NEB), 1.5 μl water and 15 μl PEG8000 (NEB). The ligation mixture was incubated at 25 °C for 2 h and 16 °C overnight. The ligation product was purified using the Zymo Oligo Clean & Concentrator kit (Zymo Research, D4060) according to the manufacturer’s instructions. The sample was eluted in 20 μl water and kept on ice prior to Bioanalyzer analysis (Agilent, small RNA kit) or used directly in the demethylation step.

tag: reference library

value: miRXplore Universal Reference sample consisting of an equimolar mixtures of 963 miRNAs from human, mouse, rat and viral sources

tag: vendor and catalog #

value: Miltenyi Biotec, catalog #:130-093-521


title: MCF10A_shR1-C4_2


title: miRXploreUR_rep3

description:
Sample 18
synthetic oligos based on miRNA sequences
RNA (synthetic, not extracted)
180719_GEO_miRNAs.txt


title: I-BET151-2

city: Paris

first: lukas

last: huijbregts

address: 123 Boulevard Port Royal

institute: INSERM

scan_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Mouse Gene 2.0 ST (Affymetrix) at 45°C for 17 hours.

data_processing:
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
The data were analyzed with R Bioconductor packages using using RMA as normalization method

source_name: Dorsal embryonic (E11.5) pancreatic bud cultured for 24h

label_protocol: Total RNA is reverse transcribed following the GeneChip™ WT PLUS Reagent Kit (applied biosystems). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 3,6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).   After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G. The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.

extract_protocol: RNeasy Micro kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Pools of 10 Dorsal embryonic pancreatic buds were cultured for 24h in presence of either 0.1% DMSO, 100nM JQ1 or 500nM I-BET151 prior to RNA extraction

tag: tissue

value: Dorsal embryonic (E11.5) pancreatic bud


title: I-BET151-1

hyb_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G. The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.


title: gDNA from subject PARVAI

treatment_protocol: Diagnostic (presentation) bone marrow or peripheral blood specimens were collected from patients prior to induction therapy. Additional genomic data types and clinical covariates are available for these specimens under the TARGET-AML study (phs000465), available through the database of genotypes and phenotypes (dbGaP) and the NCI Genomic Data Commons (GDC).

value: tumor

value: Female


title: JQ1-2


title: MCF10A_shR1-C4_1


title: JQ1-1


title: miRXploreUR_rep1

description:
Sample 16
synthetic oligos based on miRNA sequences
RNA (synthetic, not extracted)
180719_GEO_miRNAs.txt


title: CTRL-2

description: CTRL

value: CTRL (DMSO 0.1%)


title: S0_4

source_name: S. pombe_S0

value: YES (H2O)


title: MCF10A_shR1-C1_3


title: S0_3

value: wild type


title: S0_2

value: exponential phase


title: MCF10CA1a_EV_2


title: mixE_rep3

description:
Sample 15
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt

data_processing:
Processing pipeline 1: Raw reads were trimmed using tastxtoolkit/0.013. A minimum adapter alignment length of 10bp was required, and unknown (N) nucleotides were kept. Sequences were were blasted against a reference library using blast/2.6.0 with the parameters: -perc_identity 90 -word_size 9 -dust no -soft_masking false. Among multiply mapped reads, the primary alignment was selected. For reads where more than one assignment was "tied" as the primary assignment, the read was discarded.
Library strategy: AQRNA-seq
Genome_build: RNA Oligo standards, miRXplore Universal Reference
Supplementary_files_format_and_content: Tab-delimited text files containing  the names of target RNA species and their associated read counts

value: 5 synthetic RNA oligos

tag: oligo concentrations

value: 25-mer:200 fmoles; 40-mer:40 fmoles; 60-mer:80 fmoles; 80-mer #1:120 fmoles; 80-mer #2:160 fmoles


title: MCF10A_shNS_3

value: Non-Specific shRNA


title: MCF10A_shR1-C1_2


title: MCF10A_shR1-C1_1


title: gDNA from subject PASLPE

value: Male


title: mixD_rep3

description:
Sample 12
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt

value: 25-mer:160 fmoles; 40-mer:200 fmoles; 60-mer:40 fmoles; 80-mer #1:80 fmoles; 80-mer #2:120 fmoles


title: S0_1


title: mixE_rep1

description:
Sample 13
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt


title: B73-Input

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using Illumina CASAVA.
Raw reads from RIP and Input-seq data were mapped to the B73 genome using TopHat (v2.0.12) with the default parameters. The paired-end reads from anti-CENH3 RIP, input and lncRNA data were joined with SeqPrep (https://github.com/jstjohn/SeqPrep) with the parameter “-q 30 -L 25”
The gene expression levels were calculated following procedures and steps with cufflinks. The merged reads with remaining unmerged paired-end reads were used to conduct a BLAST search of the different sequences using the parameter “-e value 1e-5”.
The number of reads for each unit of the different repeat sequences was counted, and the relative enrichments of different sequences between the input and RIP samples were calculated using the ratios normalized by the total reads
Genome_build: Maize B73 RefGen_v4 and Triticum urartu genome
Supplementary_files_format_and_content: TXT files from RNA-seq data contain genes expression level. Merge fasta file.

organism: Zea mays

source_name: maize

growth_protocol: Suitable materials were planted in the greenhouse for resequencing experiments.

extract_protocol:
The leaves were then transferred to liquid nitrogen and ground into a fine powder. The following experiment was carried out using the native ChIP protocol. The chromatin was digested into single nucleosomes using 0.02 U/μl DNase I (RNase-free) at 37°C. Dynabeads Protein A (ThermoFisher, Cat#:10001D) was used for binding the anti-CENH3 antibody. After washing the beads incubated with the antibody and chromatin fragments, the beads were eluted twice at 65°C for 15 min using elution buffer containing 50 mM Tris-HCl (pH = 7.5), 10 mM EDTA, 200 mM NaCl and 1% SDS. The eluted fractions were combined, and Proteinase K (Invitrogen, Cat#: 25530-49) was added to relieve cross-linking at 37°C overnight after which the RNA was extracted using TRIzol reagent, and the residual DNA was removed using RNase-free DNase I (NEB, Cat#: M0303S).
The cDNA libraries of RIP samples were prepared using the standard manual provided in the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Cat#: E7530S).

value: young leaves


title: mixD_rep2

description:
Sample 11
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt


title: mixE_rep2

description:
Sample 14
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt


title: B73-RIP

tag: rip antibody

value: anti-CENH3 antibody


title: mixD_rep1

description:
Sample 10
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt


title: mixC_rep1

description:
Sample 7
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt

value: 25-mer:120 fmoles; 40-mer:160 fmoles; 60-mer:200 fmoles; 80-mer #1:40 fmoles; 80-mer #2:80 fmoles


title: mixC_rep3

description:
Sample 9
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt


title: mixC_rep2

description:
Sample 8
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt


title: gDNA from subject PARSAA

address: 1 Children's Way, #512-10


title: MDA-MB-231_parental_1

value: Parental


title: MCF10A_shNS_2


title: MDA-MB-231_parental_2


title: gDNA from subject PARTWN


title: MCF10CA1a_parental_3


title: MCF10A_shNS_1


title: mixB_rep2

description:
Sample 5
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt

value: 25-mer:80 fmoles; 40-mer:120 fmoles; 60-mer:160 fmoles; 80-mer #1:200 fmoles; 80-mer #2:40 fmoles


title: MCF10CA1a_parental_2


title: mixB_rep3

description:
Sample 6
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt


title: mixB_rep1

description:
Sample 4
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt


title: MCF10CA1a_parental_1


title: MDA-MB-231_parental_3


title: mixA_rep3

description:
Sample 3
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt

value: 25-mer:40 fmoles; 40-mer:80 fmoles; 60-mer:120 fmoles; 80-mer #1:160 fmoles; 80-mer #2:200 fmoles


title: MCF10AT1_parental_3


title: MCF10AT1_parental_2


title: mixA_rep2

description:
Sample 2
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt


title: MCF10AT1_parental_1


title: mixA_rep1

description:
Sample 1
synthetic oligos based on random sequences
RNA (synthetic, not extracted)
180719_GEO_standards.txt


title: 786-0, drug treated and infected_Orthovanadate

city: Ottawa

first: Mohammed

last: Selman

state: ON

address: 501 Smyth Road

department: Cancer Center

country: Canada

institute: Ottawa Hospital

description: Gene expression data from treated 786-0 cells

hyb_protocol: cRNA  was Hybridized for 16 hr at 45°C to Affymetrix Human PrimeView Array. Performed by The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Microarray data was processed using Transcriptome Analysis Console (TAC) 3.0 under default parameters of Gene Level Differential Expression Analysis.  The value definition was carried out with the Affymetrix Expression Console Software.

source_name: 786-0 cells 24 hour after vanadate treatment and  infection with VSVd51

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: 786-0 cells were grown in in HyQ high-glucose Dulbecco’s modified Eagle’s medium supplemented with 10 % fetal calf serum and incubated at 37 °C in a 5% CO2 humidified incubator.

extract_protocol: Twenty-four hours post infection, RNA was collected using an RNA-easy kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Cells were pretreated for 4hours with orthovanadate(150uM), metavanadadate (150uM) or the vehicle. Following pre-treatment, the cells were infected with VSVΔ51 at an MOI of 0.01 or left uninfected.

value: kidney

tag: cell type

value: renal cell adenocarcinoma


title: 786-0, infected_1

source_name: 786-0 cells 24 hour after infection with VSVd51


title: 786-0, drug treated and infected_Metavanadate


title: CTRL-1

description: CTRL

value: Dorsal embryonic (E11.5) pancreatic bud

value: CTRL (DMSO 0.1%)


title: 786-0, untreated_1

description: Gene expression data from 786-0 cells

source_name: 786-0 cells 24 hour after mock treatment


title: 786-0, untreated_2

description: Gene expression data from 786-0 cells


title: gDNA from subject PARAUM

extract_protocol: Starting with one vial of cryopreserved cells derived from Bone Marrow (or if Bone Marrow unavailable, Peripheral Blood), cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip.

value: tumor


title: MCF7_parental_2


title: 786-0, infected_2


title: gDNA from subject PASFYF


title: 786-0, drug treated_Metavanadate

source_name: 786-0 cells 24 hour after vanadate treatment


title: 786-0, drug treated_Orthovanadate


title: ymWT.FA2

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

institute: ASU-Banner Neurodegenerative Disease Research Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: We used the R software package, Limma, and the neqc function to perform background subtraction using the negative control probes, and quantile normalization using both positive and negative control probes.

label: Biotin

source_name: epidermis

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays (Thermo Fisher Scientific)

extract_protocol: Total RNA from murine epidermis was isolated with RiboPure kit (Ambion, Life Technologies, Grand Island, NY, USA) exactly according to the manufacturer's instructions . RNA samples were checked for quality and integrity with the Agilent 2100 bioanalyzer.

treatment_protocol: Seven-to eight-week-old mice were shaved and treated 3 days later. Glucocorticoid FA was applied topically (2 μg/animal) in 200 μl acetone to the back skin once.  Control animals were treated with acetone only. The skin samples were harvested 24 hours after the treatment.

value: male

tag: agent

value: glucocorticoid fluocinolone acetonide (FA)

tag: strain


title: MCF10A_parental_3

tag: treatment


title: MCF10A_parental_2


title: gDNA from subject PARTYK

tag: group


title: ymWT.FA1


title: ymWT2

value: Acetone


title: MCF7_parental_1


title: MCF7_parental_3


title: ymWT1


title: lung adenocarcinoma sample_IFN-γ-PD-L1- [PT 14386]

first: yi

last: gao

address: No.1095 Jie Fang Avenue

department: Thoracic surgery

institute: Tongji Hospital

description: gene expression in IIIA lung adenocarcinoma with IFN-γ low expression and PD-L1 low expression

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: IIIA lung adenocarcinoma, IFN-γ low expression, PD-L1 low expression

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

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Lung adenocarcinoma specimens were obtained from patients, who underwent pulmonary resection for lung cancer between 2012 and 2015 in the Department of Thoracic Surgery, Tongji Hospital. Each tumor sample was divided into two parts. One part of the tumor tissue was stored in liquid nitrogen for RNA and Protein extraction. The other part was fixed in 10% formalin and embedded in paraffin wax for immunohistochemistry. None of these patients received either radiation or chemotherapy before surgical operation. Histological diagnosis of tumors was based on the World Health Organization criteria. The TNM stage was determined according to the revised 2010 AJCC staging guidelines.

value: lung adenocarcinoma

tag: ifn-gamma level

value: low

tag: pd-l1 level

tag: tumor stage

value: IIIA

tag: age


title: Day12_Rep3_Vrip

city: Geneva

first: Alisson

last: Kovaleski

address: 630 W. North Street

institute: Cornell University

data_processing:
Barcode spltting: Fastx_Barcode_splitter.pl.  Raw data files were split based on custom 6bp nucleotides
Reads were quality filtered using fastq_quality_filter (-Q33 -q 25 -p 25)
Barcodes removed from each bin using fastx_trimmer  (-Q33 -f 7)
Adapter removal: cutadapt (--minimum-len 25 -O 3)
Alignment: STAR using default parameters, the 12xV2 grapevine genome and the V3 annotation file (Vitis_vinifera_gene_annotation_on_V2_v20.gff3)
Feature counting: ht-seq count (-f sam -s no -t gene)
Differential gene expression: DESeq2
Pathway Enrichment: VitisPathways
Genome_build: 12xV2 grapevine genome: https://urgi.versailles.inra.fr/Species/Vitis
Supplementary_files_format_and_content: Counts files are the output gene counts produced by htseq-count.

organism: Vitis riparia

growth_protocol: Two clonal vines of Vitis amurensis and Vitis riparia are maintained under standard vineyard conditions in the USDA cold hardy grapevine germplasm repository.  Vitis vinifera vines are grown in a commercial vineyard under standard vineyard conditions.

extract_protocol:
RNA was isolated from pulverized tissue using the Sigma Spectrum Plant total RNA isolation kit.
Libraries were constructed following a modified protocol based on Borodina et al 2011.  Methods were modified by adding 3% w/v PVP40 to the lysis buffer to help reduce extraction inhibitors.

treatment_protocol: Dormant canes were pruned from the vineyard.  Day0 buds (3 replicate buds) were cut from the cane and plunged into liquid nitrogen.  Canes were pruned to single node cuttings and placed in cups of water. Cups were placed at room temperature.  Each subsequent day, replicate buds were cut from the canes and flash frozen.  Five replicate collections were conducted on each collection day.  Buds were collected until evidence of budburst was observed for each genotype.

value: Dormant Bud

tag: genotype

tag: replicate


title: lung adenocarcinoma sample_IFN-γ-PD-L1- [PT 14279]

tag: gender


title: gDNA from subject PASMYS

tag: age at diagnosis (days)

value: Female


title: yfWT.FA2

value: female


title: gDNA from subject PASWNZ


title: Day12_Rep2_Vrip


title: Day12_Rep1_Vrip


title: lung adenocarcinoma sample_IFN-γ-PD-L1- [PT 14315]


title: MCF10A_parental_1

tag: cell line

value: Parental


title: lung adenocarcinoma sample_IFN-γ+PD-L1- [PT 14548]

description: gene expression in IIIA lung adenocarcinoma with IFN-γ high expression and PD-L1 low expression

source_name: IIIA lung adenocarcinoma, IFN-γ high expression, PD-L1 low expression

tag: tissue

value: high


title: Day11_Rep3_Vrip


title: yfWT2


title: lung adenocarcinoma sample_IFN-γ+PD-L1- [PT 15144]


title: yfWT1


title: lung adenocarcinoma sample_IFN-γ-PD-L1+ [PT 15041]

description: gene expression in IIIA lung adenocarcinoma with IFN-γ low expression and PD-L1 high expression

source_name: IIIA lung adenocarcinoma, IFN-γ low expression, PD-L1 high expression


title: yfWT.FA1


title: Day11_Rep2_Vrip


title: Day11_Rep1_Vrip