title: Bs_sys rep1

city: Cologne

first: Alga

last: Zuccaro

state: NRW

address: Zuelpicher Str. 47b

department: Botanical Institute

institute: University of Cologne

data_processing:
Genome_build: Hordeum vulgare: 160404_barley_pseudomolecules_masked;   Bipolaris sorokiniana: jgi.doe.gov Cocsa1;  Serendipita vermifera: jgi.doe.gov Sebve1
Reference Genomes: Hordeum vulgare updated version of 2016: http://webblast.ipk-gatersleben.de/barley_ibsc/downloads/)
Reference Genomes: Bipolaris sorokiniana isolate ND90Pr (Ohm et al., 2012; Condon et al., 2013)  released by JGI (https://www.ncbi.nlm.nih.gov/genome/3236, https://genome.jgi.doe.gov/portal/Cocsa1/Cocsa1.download.html)
Reference Genomes: Serendipita vermifera (MAFF305830) (Lahrmann et al., 2015). (https://www.ncbi.nlm.nih.gov/genome/18204, genome_assembly_id=218407, https://genome.jgi.doe.gov/Sebve1/Sebve1.home.html)
Processing of raw reads: Quality of raw reads was assessed using the FastQC tool v0.11.4. Paired-end and single-end reads were cleaned using the corresponding program in Trimmomatic v0.36 (Bolger et al., 2014) with the following parameters: LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:50. Bases with a quality lower than 5 were trimmed from the leading and trailing ends. Individual reads were scanned to cut along 4-mer sliding window if the average quality per base was found to be lower than 15. Only reads with a minimum length of 50 bp were selected for further analysis.
Mapping to reference genomes: Processed and filtered reads from root samples were aligned against the genomes of barley, Serendipita vermifera and B. sorokiniana, whereas reads from the fungal confrontation samples were mapped onto the fungal genomes only. Mapping was performed using the spliced aligner TopHat v2.1.0 (Kim et al., 2013) with the following parameters: --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --minimum-anchor 8 --splice-mismatches 2 --minimum-intron-length 50 --maximum-intron-length 500,000 --maximum-insertion-length 12 --maximum-deletion-length 12 --maximum-multi hits 1. Non-spliced reads for which alignments had more than 2 mismatches were discarded. Spliced reads with a minimum 8 bases that aligned on each side were kept only if the spliced alignment in the anchor region did not exceed 2 mismatches. Reads with multiple alignments mapping to different locations/genes/genomic regions were discarded. Only uniquely mapped reads were retained in the aligned BAM files.
Estimation of gene expression: The number of reads mapped per gene was counted using HTSeq-Count in the ‘Intersection Non Empty’ mode (Anders et al., 2015). Given the BAM file of aligned reads and the gene feature format (GFF) file, HTSeq counts how many reads mapped per gene and retrieves locations at which reads were mapped on a reference genome. Resulting read counts were normalized against effect of gene length and differences in total mapped reads (library size) per sample using RPKM (Reads Per Kb per Million reads) to obtain a normalized expression level of each gene per sample.
Differential gene expression analysis: Genes with a minimum of 1 RPKM in all replicates of at least one sample were used for differential expression analysis with the Bioconductor software package edgeR (v3.15.1) (Robinson et al., 2010; McCarthy et al., 2012)
Supplementary_files_format_and_content: tab-delimited text files include raw read count, RPKM values, CPM, REI values per gene per sample (Condition)
Supplementary_files_format_and_content: Bipolaris_sorokiniana_blast2GOannotation_rawrc_rpkm_rei.txt: Bipolaris sorokiniana genes; blast2GO annotations; raw read count (reads mapped to Bipolaris sorokiniana genome) per gene (annotated genes of Bipolaris sorokiniana ); normalised read count - RPKM (Reads Per Kilobase Million);  edge R normalised read count CPM (count per million); normalised Relative Expression Index REI (calculated on RPKM)
Supplementary_files_format_and_content: Hordeum_vulgare_blast2GOannotation_rawrc_rpkm_rei.txt: Hordeum vulgare genes; blast2GO annotations; raw read count (reads mapped to Hordeum vulgare genome) per gene (annotated genes of Hordeum vulgare ); normalised read count - RPKM (Reads Per Kilobase Million);  edge R normalised read count CPM (count per million); normalised Relative Expression Index REI (calculated on RPKM)
Supplementary_files_format_and_content: Serendipita_vermifera_blast2GOannotation_rawrc_rpkm_rei.txt: Serendipita vermifera  genes; blast2GO annotations; raw read count (reads mapped to Serendipita vermifera genome) per gene (annotated genes of Serendipita vermifera  ); normalised read count - RPKM (Reads Per Kilobase Million);  edge R normalised read count CPM (count per million); normalised Relative Expression Index REI (calculated on RPKM)
Supplementary_files_format_and_content: Serendipita_vermifera_JGI_geneID.txt: Serendipita vermifera transformed gene IDs (used in the study); corresponding JGI gene names; JGI transcript ID; JGI protein ID
Supplementary_files_format_and_content: Bipolaris_sorokiniana_JGI_geneID.txt: Bipolaris sorokiniana transformed gene IDs (used in the study); corresponding JGI gene names; JGI transcript ID; JGI protein ID

organism: Hordeum vulgare

source_name: Hordeum vulgare roots

growth_protocol:
Natural ’Cologne soil’ (CS) was collected at the Max Planck Institute for Plant Breeding Research (50.958 North / 6.856 East, Cologne, Germany) in March and in September 2010 from experimental agricultural sites that were not exposed to agrochemicals for several years, stored and prepared for use as previously described (Bulgarelli et al. 2012. Nature 488(7409): 91-95. DOI: 10.1038/nature11336). Mixed mycelial confrontation in soil: Transgenic Serendipita vermifera (MAFF305830) expressing GFP and B. sorokiniana ND90Pr were pre-cultured in liquid MYP medium at 28°C, continuously shaking at 120 rpm for 6 and 4 days, respectively. For mixed inoculation of sterile Cologne soil, mycelia were mixed at a 1:1 (w/w) ratio and re-suspended in sterile distilled water to a final concentration of 250 mg mL-1. Sterile Petri dishes were filled with sterile soil and mycelial suspensions were added onto the soil surface. As controls, the same amount of mycelium of each fungus was re-suspended in sterile distilled water and spread over the soil surface. Following 2 days of incubation at 28°C in the dark, fungal mycelia were harvested from the soil surface and snap-frozen in liquid nitrogen for RNA extraction. Plant-fungi tripartite interaction in soil: Mycelial suspensions of GFP-expressing Serendipita vermifera (40 mg mL-1) and conidia of B. sorokiniana (3.4x104 spores/mL) were used to inoculate roots of 7-day-old barley seedlings (Hordeum vulgare cv. Golden Promise) either in combination or alone. For endophyte inoculations, roots were dipped into mycelial suspensions of Serendipita vermifera. Plantlets were placed into split-root chambers where both sides were filled with 250 mL of the 1:1 sterile Cologne soil:sand mix. For inoculations with B. sorokiniana, 30 mL conidia suspensions were distributed over the surface of the soil:sand mix covering the root. For mock controls, distilled water was used as treatment. Six plants were used for each treatment in the split-root experiment. Separate sides of the split-root chambers were considered independent treatments. Roots were harvested at 6 dpi, washed thoroughly and root segments were collected. Four cm root segments from soil-grown plants were removed 5 cm below the root-shoot junction. Plant material from the same treatment was pooled and snap-frozen in liquid nitrogen.
6 days after inoculation; 7 days old seedlings transferred into split-root chambers with natural soil (sterile) and cultivated in a growth chamber with a day/night cycle of 16/8 h at 22/18°C, 60% humidity and a light intensity of 108 µmol m-2 s-1

extract_protocol:
Hyphae were flash frozen and RNA was harvested using Nucleospin RNA Plant kit (Macherey-Nagel, Germany). Roots were flash frozen and RNA extracted using TRIzol reagent.  Illumina TruSeq RNA Sample Prep Kit was used with 1 - 3ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols; Illumina TruSeq RNA Sample Prep Kit was used with the total RNA upto 2µg from the “confrontation in soil” and upto 3µg from the “tripartite interaction in soil” experiments in order to construct the sequencing libraries.

tag: experiment

value: tripartite interaction in soil

tag: age

value: 7 days old seedlings transferred to soil and sampled  6 days later after inoculation

tag: growth

value: 4 days old seedlings transferred into split-root chambers with natural soil (RT)

value: Hordeum vulgare roots inoculated with Bipolaris sorokiniana (systemic)


title: CuO NH3 10 S3

status: Public on Jul 06 2019

type: RNA

city: Helsinki

first: Harri

last: Alenius

address: Haartmaninkatu 3

department: Human Microbiome Research Program

country: Finland

institute: University of Helsinki

description: PBS-challenged, exposed to 10 μg/day of CuO NH3, replicate 3

hyb_protocol: Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays according to the manufacturer's recommendations.

scan_protocol: Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and analyzed with BioConductor package Limma.

molecule: total RNA

organism: Mus musculus

source_name: Lung tissue

label_protocol: Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.

growth_protocol: Female BALB/c mice (6-8 weeks old) were housed in groups of four in stainless steel cages, bedded with aspen chip and were provided with standard mouse chow diet and tab water ad lib. 12 h dark/light cycle was used in the animal room temperature being 20-21 degree celcius and humidity of 40-45 %.

extract_protocol: Lung samples were homogenized in TRIsure reagent and total RNA extraction was performed following the instructions provided by the manufacturer. Quantity and quality of the samples was determined by NanoDrop spectrophotometer and Agilent Bioanalyzer 2100, respectively. Samples with RNA integrity number > 8 were selected and independent pools of two RNA samples were used for the analysis.

treatment_protocol: Mice were exposed to CuO, CuO COOH, CuO NH3 or CuO PEG at three doses, 2.5, 10 and 40 mg/mouse/administration via oropharyngeal aspiration on four consecutive days in a mouse model of asthma. Lung tissue samples were collected 24 h after the final exposure, stabilized in RNAlater overnight and stored thereafter at -70ºC.

tag: strain

value: BALB/c

tag: gender

value: Female

tag: sensitization

value: OVA/Alum

tag: challenge

value: PBS

tag: nanomaterial

value: CuO NH3

tag: daily dose


title: CuO NH3 40 S2

description: PBS-challenged, exposed to 40 μg/day of CuO NH3, replicate 2


title: Bs_sys rep3

type: SRA

country: Germany

library_source: transcriptomic

tag: treatment


title: Sv_sys rep3

value: Hordeum vulgare inoculated with Serendipita vermifera (systemic)


title: human macrophages untreated [GCS61089]

city: Shanghai

first: Xinxin

last: Hou

address: 1200 Cailun Road

country: China

institute: Shanghai University of Traditional Chinese Medicine

hyb_protocol: Following fragmentation, 5.2 ug of cRNA were hybridized for 16 hr at 45℃ according to Affymetrix WT PLUS Reagent Kit User Manual using the GeneChip Hybridization Wash and Stain Kit. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using AGCC Scan Control Software on the Affymetrix Genechip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Homo sapiens

source_name: human macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary collection and culture of human peripheral blood monocytes. Monocytes were further differentiated into macrophages (monocyte-derived macrophage, MDM) by incubation with M-CSF for 6 days. The macrophages were cultured in cell culture incubator.

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

treatment_protocol: The macrophages were culutred in RPMI-1640 with 10% FBS, rhFGL2 (1 µg/ml, Abnova) or the same volume of PBS (as control) were added for 24h, then the cells were placed on ice in the Trizol solution (GibcoBRL).

tag: subject status

value: healthy volunteer

tag: ethnicity

value: Chinese

tag: tissue

value: Peripheral blood

tag: cell type

value: monocyte-derived macrophage (MDM)

value: PBS for 24hrs


title: Bs_sys rep2


title: OVA S1

description: OVA-challenged control, replicate 1

value: OVA


title: ATACseq_EPC_nodox_rep2

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

country: USA

institute: University of Minnesota

description: Doxycycline-inducible embryonic stem cells.

library_source: genomic

data_processing:
ChIP-seq analysis: Each sample’s reads were aligned to the mouse (mm10) genome using Bowtie2 followed by removal of PCR duplicates using Samtools. Peak calling was performed using MACS with the following parameters: --bw 300 -p 1e-3. To identify the list of high confidence mouse Sox7 peaks we performed 4 independent ChIP-seq experiments and, using the bedtools intersect function, only common regions between 2 experiments were further considered. In addition, the Sox7 peak list was filtered (intersect –v option) for sites overlapping to peaks detected in the uninduced control ChIP-seq and input sample. Bigwig files for visualization on IGV were generated by converting the wig files obtained from MACS using the Kent tool Wig-to-BigWig.
ATAC-seq analysis: Reads were aligned to the mouse genome (mm10) using Bowtie2 with the following parameters: -q -I 38 -X 2000 --local --dovetail --no-mixed --no-discordant. Aligned reads were filtered for PCR duplicates using Samtools and then processed with MACS 1.4 with the following parameters: --nomodel --nolambda --keep-dup all --call-subpeaks -p 1e-4 -w –S. Bigwig files for visualization on IGV were generated by converting the wig files obtained from MACS using the Kent tool Wig-to-BigWig. ATAC-seq reads overlapping to Pax3 peaks were retrieved using the R Bioconductor package and then used to generate density maps with Seqminer. To identify differentially accessible peaks, we used the BEDTools intersect function: the common regions (-f 0.5 -F 0.5 -e options) for the dox-induced samples were intersected (-v -f 0.2 options) with the combined list of control peaks (from non-induced cells).
Mouse RNA-seq analysis: FASTQ files were trimmed for quality using trimmomatic and aligned to the mm10 genome using HISAT2. Raw counts per gene were assigned using subread featurecounts and used as input for differential gene expression analysis in edgeR via the CLC genomics workbench.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: ChIP-seq: Processed files represent list of peaks 1) identified by MACS in each replicate; 2) Sox7 peaks detected indox-induced samples after removing peaks called in non-induced samples and input; 3) Sox7 peaks overlapping to Gata4 sites.
Supplementary_files_format_and_content: ATAC-seq: Processed files contain 1) the list of peaks identified by MACS in each replicate and 2) the list of CPC +dox and EPC +dox specific accessible loci.
Supplementary_files_format_and_content: RNA-seq: Processed file contains tab-delimited expression values following analysis using EdgeR.

molecule: genomic DNA

source_name: differentiating mES cells

growth_protocol: Mouse ES cell differentiation was achieved by diluting cells to 10,000 cells/ml in EB differentiation medium following incubation at 37°C as hanging drops in non-adherent Petri dishes (10μl/drop equivalent to 100 cells). EB differentiation medium: IMDM supplemented with 15% FBS, 1% Penicillin/Streptomycin, 2mM Glutamax, 50 μg/ml Ascorbic acid, 4.5 mM Monothioglycerol and 200μg/ml iron-saturated transferrin. After 2 days, EBs were recovered by flushing plates with PBS, resuspended in EB medium and incubated in an orbital shaker at 80 RPM, 37°C. Transgene induction was achieved by adding doxycycline for 24 hrs (Sigma-Aldrich) to day 3 EBs cultures (final concentration 1µg/ml). Medium was replaced every two days through the differentiation protocol. At day 4, EBs were disaggregated and single cells were incubated for 20 minutes with PDGFRα-PE and FLK1-APC conjugated antibodies. PDGFRα+FLK1- cells were sorted using FACSAriaII (BD biosciences). The dox inducible cell line A2lox-Sox7-Myc derived from E14Tg2a (parental) were used to make all EBs.

extract_protocol:
ChIP-seq: Day 4 EBs were prepared for ChIP from doxycycline treated (24 hrs) and untreated (control) conditions. Day 4 EBs were dissociated with trypsin/EDTA solutionvat 37°C for 1.5 min with gentle shaking and reaction was inhibited by adding 10% FBS/PBS. Washed cells were treated with 1% formaldehyde (Pierce) to crosslink protein-DNA complexes (10 min at RT) followed by quenching with glycine. Cell pellets were incubated sequentially in lysis buffers 1, 2, 3 supplemented with protease inhibitors (complete-mini protease inhibitor cocktail (Roche)) for 10 min each at 4°C (LB1: 50mM HEPES KOH, pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100; LB2: 10mM Tris-HCl, pH 8, 200mM NaCl, 1mM EDTA, 0.5 mM EGTA; LB3: 10mM Tris-HCl, pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine) and then sonicated for four cycles with a probe tip sonicator at 18% power for 1 min with intervals of 10 s ON-10 s OFF to reach an average chromatin size of 300bp. After shearing, samples were centrifuged for 10 min at 16,000g and snap-frozen in liquid nitrogen if not processed immediately. For each ChIP, 25mg of chromatin was precleared for 4 hr at 4°C with 15µl of BSA-blocked Protein A-conjugated sepharose beads (GE healthcare) and then supplemented with 1/10 volume of 10% Triton X-100. Immunoprecipitation was performed by overnight incubation with normal mouse IgG (5µg - Millipore) or anti-myc antibody (5µg clone 9E10 – Roche). Immune complexes were recovered by incubation with 15µl of BSA-blocked Protein A-conjugated sepharose beads for 4 hr at 4°C and then washed five times with RIPA wash buffer (50mM HEPES KOH, pH7.5, 500mM LiCl, 1 mM EDTA, 1% NP40, 0.25% Triton X-100 and 0.7% sodium deoxycholate) and one time with TEN buffer (10mM Tris-HCl, pH 8, 1mM EDTA and 50mM NaCl). Immunoprecipitated chromatin was recovered by incubating beads with 200µl of elution buffer (50mM Tris-HCl, pH 8, 10mM EDTA and 1% SDS) for 20 min at 65°C. Chromatin from immunoprecipitation and input (equivalent to 1% of starting material) was reverse crosslinked overnight at 65°C, then diluted 1:1 with TE (10mM Tris-HCl, pH 8, and 1mM EDTA) supplemented with 4µl of RNaseA (20mg/ml – ThermoFisher) and incubated for 2 hr at 37°C followed by Proteinase K treatment (4µl of 20mg/ml) for 30 min at 55°C. DNA was purified using Phenol-chloroform-isoamyl alcohol extraction, precipitated, washed, and dissolved in 50µl H2O.
ChIP-seq libraries were generated using the NEBNext DNA library prep kit (NEB) and AMPure XP beads (Beckman Coulter) for all the purification and size selection steps. 10ng or less of DNA were processed following manufacturer's instructions.
ATAC-seq: 50,000 freshly sorted cells from differentiated ES cultures were washed with 200 µl of cold PBS then resuspended in 100 µl of cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630), spun at 500 g for 10 minutes at 4°C and resuspended in 50 µl of the transposition reaction mix. Transposition occurred at 37°C for 30 minutes, after which transposed DNA was purified using a Qiagen MinElute Kit and eluted in 10µl Elution Buffer. Final libraries were generated by primer extension of the transposed DNA followed by PCR amplification using Illumina-compatible adapter-barcodes.
RNA-seq: d4 EBs were collected and RNA was prepared using the Purelink RNA mini kit (ThermoFisher).
RNA-seq libraries were generated using the TruSeq stranded kit and dual-index adapter-barcodes following manufacturer's instructions.

tag: cell line

value: A2lox-Sox7-Myc (derived from E14Tg2a)

tag: doxycycline-treatment

value: Not treated

tag: purification

value: PDGFRalpha-FLK1+ sorted

value: Day 4 EB


title: NO2

city: Cambridge

first: Kevin

last: Chalut

address: Tennis Court Road

department: Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
1. Trimmomatic adaptor clipping for TruSeq-HT adapters.
2. Hisat2 alignment to rat genome Rn6 paired end
3. Stringtie
4. Bowtie
Genome_build: RN6
Supplementary_files_format_and_content: All processed data files are supplied in the GTF format.

organism: Rattus norvegicus

source_name: Cultured neonate OPCs soft hydrogel

growth_protocol: MACs sorted OPCs cultured  in FGF and PDGF

extract_protocol:
Zymo Directzol RNA microkit
SMARTer Stranded Total RNA-pico Input Mammalian Kit

treatment_protocol: OPCs were cultured on laminin coated hydrogels of differing stiffness

value: Cultured neonate OPCs soft hydrogel


title: Hv_mock rep3

tag: experiment

value: tripartite interaction in soil

value: 7 days old seedlings transferred to soil and sampled  6 days later

value: 4 days old seedlings transferred into split-root chambers with natural soil (RT)


title: CuO PEG 40 + OVA S3

description: OVA-challenged, exposed to 40 μg/day of CuO PEG, replicate 3

value: BALB/c

value: Female

value: OVA/Alum

value: CuO PEG


title: Hv_mock rep2

tag: age


title: Hv_mock rep1

tag: growth


title: AT3

source_name: Cultured aged OPCs stiff hydrogel

value: Cultured aged OPCs stiff hydrogel


title: ATACseq_CPC_plusdox_rep2

value: PDGFRalpha+FLK1+ sorted


title: ATACseq_EPC_nodox_rep1


title: AT2


title: Bs_loc + Sv_sys rep3

organism:
Hordeum vulgare
Bipolaris sorokiniana

source_name: Hordeum vulgare roots inoculated with Bipolaris sorokiniana

value: 7 days old seedlings transferred to soil and sampled  6 days later after inoculation

value: Hordeum vulgare roots inoculated with Serendipita vermifera (systemic) and Bipolaris sorokiniana (local)


title: Bs_loc + Sv_sys rep2


title: Sv_sys rep2

value: Hordeum vulgare inoculated with Serendipita vermifera (systemic)


title: Bs_loc rep3

value: Hordeum vulgare roots inoculated with Bipolaris sorokiniana (local)


title: Bs_loc rep2


title: ATACseq_CPC_plusdox_rep1

value: A2lox-Sox7-Myc (derived from E14Tg2a)


title: Sv_sys rep1


title: Bs_loc + Sv_sys rep1


title: ATACseq_CPC_nodox_rep2

value: Not treated


title: Bs_loc rep1


title: Sv_loc + Bs_sys rep3

organism:
Hordeum vulgare
Serendipita vermifera

value: Hordeum vulgare roots inoculated with Serendipita vermifera (local) and Bipolaris sorokiniana (systemic)


title: Sv_loc + Bs_sys rep2

source_name: Hordeum vulgare roots inoculated with Serendipita vermifera


title: AO2

source_name: Cultured aged OPCs soft hydrogel

value: Cultured aged OPCs soft hydrogel


title: AO3


title: Input_rep1

value: Unsorted

value: Day 4 EB

tag: chip antibody


title: Sv_loc + Bs_sys rep1

value: tripartite interaction in soil

value: 4 days old seedlings transferred into split-root chambers with natural soil (RT)


title: ChIPseq_1day_dox_rep4

value: Anti-myc


title: Sv_loc rep3

value: Hordeum vulgare inoculated with Serendipita vermifera (local)


title: AO1


title: Bs rep3

organism: Bipolaris sorokiniana

source_name: Bipolaris sorokiniana mycelium

value: soil

value: 2 days

value: mycelium  in natural soil at room temperature (RT)


title: Sv_loc rep1

value: 7 days old seedlings transferred to soil and sampled  6 days later after inoculation


title: ChIPseq_1day_dox_rep3


title: N3

source_name: primary MACs sorted OPC

value: primary MACs sorted OPC


title: ChIPseq_1day_dox_rep2


title: Sv_loc + Bs_loc rep2

organism:
Hordeum vulgare
Bipolaris sorokiniana
Serendipita vermifera

source_name: Hordeum vulgare roots inoculated with Bipolaris sorokiniana and Serendipita vermifera

value: Hordeum vulgare roots inoculated with Bipolaris sorokiniana (local) and Serendipita vermifera (local)


title: ChIPseq_1day_dox_rep1


title: ATACseq_CPC_nodox_rep1

value: PDGFRalpha+FLK1+ sorted


title: Bs rep2


title: Bs rep1


title: Sv_loc rep2


title: AT1

value: Cultured aged OPCs stiff hydrogel


title: Sv + Bs rep2

organism:
Bipolaris sorokiniana
Serendipita vermifera

source_name: Serendipita vermifera + Bipolaris sorokiniana  mycelium

value: confrontation in soil

value: Bipolaris sorokiniana + Serendipita vermifera mycelia pre-mixed


title: N1


title: Sv_loc + Bs_loc rep1


title: Sv rep3

organism: Serendipita vermifera

source_name: Serendipita vermifera mycelium


title: ChIPseq_nodox_rep4

value: A2lox-Sox7-Myc (derived from E14Tg2a)

value: Not treated


title: ChIPseq_nodox_rep3

value: Unsorted

value: Day 4 EB


title: Sv rep2


title: KO-RS-3

status: Public on Jul 05 2019

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were trimmed for adapter sequence using trim_galore v0.5.0, then mapped to mm9 with STAR v2.6.0
Raw read counts of mm9 RefSeq annotated genes were generated by featureCounts v1.5.3 with parameters -p -C, and only uniquely mapped reads were counted.
Differential expressed genes were analyzed by DESeq2 with default parameters, genes with log2 fold change above 1 (up-regulated in KO) or below -1 (down-regulated in KO) and adjusted p-value less than 0.05 were identified as differential expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: Track files  were generated using bedtools genomecov v2.27.1 with -split and then coverted to bigwig format with bedGraphToBigWig, the values in bigwig files represent the raw read coverage without any normalization.

source_name: round spermatids from Phf7 knockout female

growth_protocol: Round spermatids were isolated from testes of WT and Phf7 knockout mice according to reported protocol (Bastos et al., 2005).

extract_protocol:
Round spermatids were flash frozen on dry ice, and RNA was harvested using Trizol reagent.1 ug of RNA for each sample was processed with the NEBNext PolyA mRNA Magnetic Isolation Module (NEB, E7490) and further processed with the NEBNext Ultra Directional RNA Library Prep kit (NEB, E7420S) or 3‘ mRNA-Seq Library Prep Kit (lexogen 015UG009V0211).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: Phf7 knockout

tag: week old

tag: tissue/cell type

value: round spermatids


title: ChIPseq_nodox_rep2

value: Anti-myc


title: Sv rep1

value: soil


title: ChIPseq_nodox_rep1


title: Sv + Bs rep1

value: 2 days


title: KO-RS-1


title: WT-RS-3

source_name: round spermatids from WT female

value: wild type


title: N2


title: WT-RS-2


title: KO-RS-2


title: WT-RS-1


title: Sv_loc + Bs_loc rep3

value: tripartite interaction in soil

value: 7 days old seedlings transferred to soil and sampled  6 days later after inoculation

value: 4 days old seedlings transferred into split-root chambers with natural soil (RT)


title: Sv + Bs rep3

value: mycelium  in natural soil at room temperature (RT)


title: NO1

value: Cultured neonate OPCs soft hydrogel


title: Cirrhotic-Pt51

city: Barcelona

first: Sara

last: Torrecilla

state: Catalonia

address: Rossello Street, 149

country: Spain

institute: IDIBAPS

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Raw data were normalized using cubic spline algorithm implemented in the Illumina Normalizer module of the GenePattern analysis toolkit (www.broadinstitute.org/genepattern) as previously described (Sia D et al, Gastroenterology, 2013).

source_name: Non-tumor cirrhotic liver

label_protocol: Standard Illumina protocol

extract_protocol: RNA extraction was performed on four to six macrodissected sections (5 μm) from each FFPE block using the automated procedure QIAcube and QIAGEN spin columns (Qiagen, Hilden, Germany). Total RNA (500ng) was used for whole-genome gene-expression profiling.

tag: pathologic classification

value: Cirrhosis

tag: tissue type

value: FFPE


title: Cirrhotic-Pt53


title: Cirrhotic-Pt3_1


title: Cirrhotic-Pt13


title: Cirrhotic-Pt6


title: Cirrhotic-Pt48


title: Cirrhotic-Pt47


title: Cirrhotic-Pt49


title: Cirrhotic-Pt52


title: Cirrhotic-Pt38


title: Cirrhotic-Pt41


title: Cirrhotic-Pt42


title: Cirrhotic-Pt43


title: Cirrhotic-Pt37


title: Cirrhotic-Pt39


title: Cirrhotic-Pt34


title: Cirrhotic-Pt100


title: Cirrhotic-Pt35


title: Cirrhotic-Pt36


title: Cirrhotic-Pt45


title: Cirrhotic-Pt30


title: Cirrhotic-Pt33


title: Cirrhotic-Pt32


title: Cirrhotic-Pt29


title: Cirrhotic-Pt50


title: Cirrhotic-Pt27


title: Cirrhotic-Pt46


title: Cirrhotic-Pt28


title: Cirrhotic-Pt26


title: Dysplastic-Pt6

source_name: Pre-malignant dysplastic nodule from cirrhotic liver

value: Dysplasia


title: sHCC-Pt52

source_name: HCC tissue from cirrhotic liver

value: Tumor


title: Dysplastic-Pt3_1


title: sHCC-Pt51


title: sHCC-Pt53


title: sHCC-Pt49


title: sHCC-Pt46


title: sHCC-Pt47


title: Cirrhotic-Pt40


title: sHCC-Pt50


title: sHCC-Pt45


title: sHCC-Pt40


title: sHCC-Pt41


title: sHCC-Pt39


title: sHCC-Pt38


title: sHCC-Pt100


title: sHCC-Pt37


title: sHCC-Pt34


title: sHCC-Pt32


title: sHCC-Pt36


title: sHCC-Pt35


title: sHCC-Pt30


title: sHCC-Pt43


title: sHCC-Pt29


title: sHCC-Pt42


title: sHCC-Pt28


title: sHCC-Pt27


title: sHCC-Pt33


title: Normal_Tissue_5

source_name: Non-tumor non-cirrhotic liver

value: Liver normal


title: sHCC-Pt48


title: Cirrhotic-Pt73

value: Cirrhotic


title: sHCC-Pt26


title: Normal_Tissue_6


title: Normal_Tissue_2


title: Normal_Tissue_4


title: Normal_Tissue_3


title: Cirrhotic-Pt72


title: Cirrhotic-Pt60


title: Cirrhotic-Pt63


title: Cirrhotic-Pt70


title: Cirrhotic-Pt68


title: Cirrhotic-Pt62


title: Cirrhotic-Pt69


title: Cirrhotic-Pt65


title: Cirrhotic-Pt58


title: Dysplastic2-Pt74


title: Cirrhotic-Pt61


title: Normal_Tissue_1


title: Cirrhotic-Pt56


title: Cirrhotic-Pt64


title: Cirrhotic-Pt74


title: Cirrhotic-Pt55


title: Dysplastic1-Pt73


title: Dysplastic2-Pt73


title: Dysplastic1-Pt74


title: Cirrhotic-Pt54


title: Cirrhotic-Pt67


title: Dysplastic-Pt70


title: Dysplastic1-Pt72


title: Dysplastic-Pt68


title: Cirrhotic-Pt59


title: Dysplastic2-Pt72


title: Dysplastic-Pt61


title: Dysplastic-Pt59


title: Dysplastic-Pt56


title: Dysplastic-Pt62


title: Dysplastic-Pt54


title: sHCC1-Pt74


title: Dysplastic-Pt55


title: Dysplastic-Pt63


title: Dysplastic-Pt64


title: sHCC2-Pt74


title: Cirrhotic-Pt3


title: sHCC2-Pt73


title: Dysplastic-Pt58


title: Dysplastic-Pt69


title: Dysplastic-Pt65


title: sHCC1-Pt73


title: Dysplastic-Pt3


title: Dysplastic-Pt60


title: sHCC1-Pt72


title: Cirrhotic_Pt-463_gene_expression

description:
Sample name: NY2173
RNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)

value: Non-tumor cirrhotic liver

tag: tissue preparation


title: Dysplastic-Pt67


title: sHCC-Pt69


title: sHCC-Pt68


title: Cirrhotic_Pt-344_gene_expression

description:
Sample name: NY2201
RNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: sHCC-Pt70


title: Cirrhotic_Pt-196_gene_expression

description:
Sample name: NY2194
RNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Cirrhotic_Pt-179_gene_expression

description:
Sample name: NY2184
RNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: sHCC-Pt65


title: Cirrhotic_Pt-422_gene_expression

description:
Sample name: NY2169
RNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: sHCC-Pt62


title: sHCC-Pt64


title: sHCC2-Pt72


title: sHCC-Pt61


title: sHCC-Pt63


title: sHCC-Pt67


title: sHCC-Pt59


title: Cirrhotic_Pt-181_gene_expression

description:
Sample name: NY2177
RNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Cirrhotic_Pt-462_gene_expression

description:
Sample name: NY2132
RNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Cirrhotic_Pt-186_gene_expression

description:
Sample name: NY2062
RNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor2_Pt-344_gene_expression

description:
Sample name: NY2203
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)

source_name: HCC tissue from cirrotic liver

value: HCC tissue from cirrotic liver


title: Cirrhotic_Pt-459_gene_expression

description:
Sample name: NY2188
RNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: sHCC-Pt60


title: Cirrhotic_Pt-356_gene_expression

description:
Sample name: NY2027
RNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Cirrhotic_Pt-457_gene_expression

description:
Sample name: NY2005
RNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: sHCC-Pt56


title: Tumor3_Pt-461_gene_expression

description:
Sample name: NY2200
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Cirrhotic_Pt-344

type: genomic

description:
Sample name: NY2201
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).

data_processing: Genotype, Log R ratio (LRR, reflecting total copy number) and B-allele frequency (BAF) obtained from GenomeStudio.

label: C-Bio and A-DNP

extract_protocol: Genomic DNA was extracted from seven to ten macrodissected FFPE sections (5 μm) using the automated procedure QIAcube and QIAGEN spin columns (Qiagen, Hilden, Germany).

treatment_protocol: Previous treatment with the Infinium FFPE restoration kit (Illumina) was performed for FFPE samples.


title: sHCC-Pt58


title: Tumor1_Pt-344_gene_expression

description:
Sample name: NY2202
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Cirrhotic_Pt-461

description:
Sample name: NY2197
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Cirrhotic_Pt-357_gene_expression

description:
Sample name: NY2100
RNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: sHCC-Pt54


title: Cirrhotic_Pt-459

description:
Sample name: NY2188
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: sHCC-Pt55


title: Tumor1_Pt-461_gene_expression

description:
Sample name: NY2198
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Cirrhotic_Pt-463

description:
Sample name: NY2173
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Cirrhotic_Pt-181

description:
Sample name: NY2177
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Cirrhotic_Pt-460

description:
Sample name: NY2180
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor3_Pt-463_gene_expression

description:
Sample name: NY2176
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Cirrhotic_Pt-179

description:
Sample name: NY2184
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Cirrhotic_Pt-422

description:
Sample name: NY2169
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Cirrhotic_Pt-196

description:
Sample name: NY2194
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Cirrhotic_Pt-458

description:
Sample name: NY2166
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-463_gene_expression

description:
Sample name: NY2175
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor1_Pt-463_gene_expression

description:
Sample name: NY2174
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Cirrhotic_Pt-357

description:
Sample name: NY2100
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Cirrhotic_Pt-462

description:
Sample name: NY2132
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Cirrhotic_Pt-448

description:
Sample name: NY2086
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor3_Pt-422_gene_expression

description:
Sample name: NY2172
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor2_Pt-422_gene_expression

description:
Sample name: NY2171
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor1_Pt-422_gene_expression

description:
Sample name: NY2170
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor2_Pt-179_gene_expression

description:
Sample name: NY2187
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor1_Pt-196_gene_expression

description:
Sample name: NY2195
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor1_Pt-179_gene_expression

description:
Sample name: NY2185
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Cirrhotic_Pt-356

description:
Sample name: NY2027
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Cirrhotic_Pt-186

description:
Sample name: NY2062
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-459_gene_expression

description:
Sample name: NY2189
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor2_Pt-459_gene_expression

description:
Sample name: NY2190
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Cirrhotic_Pt-457

description:
Sample name: NY2005
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor3_Pt-460_gene_expression

description:
Sample name: NY2183
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Cirrhotic_Pt-215

description:
Sample name: NY2010
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-344

description:
Sample name: NY2203
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-196_gene_expression

description:
Sample name: NY2196
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor1_Pt-460_gene_expression

description:
Sample name: NY2181
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor1_Pt-181_gene_expression

description:
Sample name: NY2178
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor2_Pt-458_gene_expression

description:
Sample name: NY2168
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor2_Pt-181_gene_expression

description:
Sample name: NY2179
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor2_Pt-460_gene_expression

description:
Sample name: NY2182
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor1_Pt-461

description:
Sample name: NY2198
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-461

description:
Sample name: NY2199
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor3_Pt-461

description:
Sample name: NY2200
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-196

description:
Sample name: NY2196
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-196

description:
Sample name: NY2195
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-459

description:
Sample name: NY2190
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-459

description:
Sample name: NY2189
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-179

description:
Sample name: NY2187
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-179

description:
Sample name: NY2185
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-458_gene_expression

description:
Sample name: NY2167
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor2_Pt-462_gene_expression

description:
Sample name: NY2134
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor2_Pt-357_gene_expression

description:
Sample name: NY2102
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor2_Pt-186_gene_expression

description:
Sample name: NY2064
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor1_Pt-462_gene_expression

description:
Sample name: NY2133
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor3_Pt-460

description:
Sample name: NY2183
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-460

description:
Sample name: NY2181
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-448_gene_expression

description:
Sample name: NY2087
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor2_Pt-181

description:
Sample name: NY2179
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-356_gene_expression

description:
Sample name: NY2029
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor1_Pt-186_gene_expression

description:
Sample name: NY2063
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor1_Pt-356_gene_expression

description:
Sample name: NY2028
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor2_Pt-457_gene_expression

description:
Sample name: NY2007
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor1_Pt-357_gene_expression

description:
Sample name: NY2101
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor1_Pt-181

description:
Sample name: NY2178
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: KT;Lkb1f/f#2

city: Stanford

first: Christopher

last: Murray

state: California

address: 1291 Welch Rd. B261, Beckman Center

department: Genetics

institute: Stanford University

data_processing:
Fastqs from each of two lanes were concatenated for each sample. Reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 mouse genome using STAR aligner (2.4.2a)
The number of reads uniquely aligned to exons of individual genes was determined using “intersection-nonempty” mode with HTSeq against the UCSC KnownGene (mm10) transcriptome
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delmiited text file containing genes by samples count matrix generated by HTSeq

molecule: polyA RNA

source_name: Sorted Lung Cancer Cells

extract_protocol:
Tumors were dissociated using collagenase IV, dispase, and trypsin at 37C for 30 minutes. Cells were stained for CD45 (30-F11), CD31 (390), F4/80 (BM8), and Ter119 to exclude hematopoietic and endothelial cells. FACSAria™ sorters (BD Biosciences) were used for cell sorting. Total RNA was prepared from 2.50E+04 to 6.00E+04 cells using the Qiagen RNeasy micro kit.
RNA quality was assessed using the RNA6000 PicoAssay kit on the Agilent Bioanalyzer 2100. Total RNA (30 ng/sample) was used for cDNA synthesis using the Ovation® RNA-Seq. Two micrograms of amplified double-stranded cDNA was sheared using a Covaris sonicator to an average length of 400 bp and subjected to library preparation using the Illumina TruSeqTM DNA sample preparation kit and sequenced (2×100 bp) on an Illumina HiSeq 4000.

value: lung cancer

value: KLT 755 T4

tag: genotype

tag: strain

value: mixed BL6/129


title: KT;H11LSL-Cas9_sgSik1-3#1

tag: tissue

value: KTC Sik3x T5


title: KT#4

value: KT Lenti Cre 5

value: KT


title: Tumor3_Pt-463

description:
Sample name: NY2176
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-457_gene_expression

description:
Sample name: NY2006
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: KT;H11LSL-Cas9_sgSik1-3#2

value: KTC Sik3x T1


title: Cirrhotic_Pt-448_gene_expression

description:
Sample name: NY2086
RNA extracted from non-tumoral cirrhotic tissue was genotyped with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: KT;H11LSL-Cas9_sgSik1#1

value: KTC Sik1 T3


title: Tumor2_Pt-463

description:
Sample name: NY2175
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-422

description:
Sample name: NY2171
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-463

description:
Sample name: NY2174
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-448_gene_expression

description:
Sample name: NY2088
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)


title: Tumor3_Pt-422

description:
Sample name: NY2172
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: KT#3

value: KT Lenti Cre 2


title: Tumor2_Pt-460

description:
Sample name: NY2182
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: KT;H11LSL-Cas9_sgSik1#2

value: KTC Sik1 T1


title: KT;H11LSL-Cas9_sgSik1#3

value: KTC Sik1 T2


title: Tumor2_Pt-458

description:
Sample name: NY2168
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).

value: FFPE


title: Tumor1_Pt-422

description:
Sample name: NY2170
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).

value: Tumor


title: KT#2

value: KT Lenti Cre 1


title: KT;Lkb1f/f#3


title: KT#1

value: DC0182 KT


title: KT;Lkb1f/f#1

value: KLT 688 T1


title: Tumor2_Pt-357

description:
Sample name: NY2102
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).

value: HCC tissue from cirrotic liver


title: KNOCKOUT 4

city: Chicago

first: Yan

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

data_processing:
Raw sequencing QC assessement: FastQC v0.11.2
Alignment: STAR v2.4.0g1
Customized sample merged reference genome for transcripts assembly with featureCounts: cufflinks cuffmerge
Samples gene transcripts assembly: featureCounts
Differentially expressed genes analysis: edgeR
Genome_build: UCSC mouse genome model: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample.
Supplementary_files_format_and_content: customized sample merged reference gtf for featureCounts, gtf file

source_name: knock out_adipose tissue

growth_protocol: Prior to sacrifice at 20 weeks of age, wildtype and knockout mice were placed on a 45% high-fat diet for twelve weeks, between ages 8-20 weeks old

extract_protocol:
Primary adipose tissue was immediately homogenized; RNA was then collected from the slurry using a commercially available kit (E.Z.N.A Total RNA Kit, Omega Bio-Tek, GA) per manufacturer’s instructions. Samples were then prepared for RNAseq on the Illumina HiSeq4000 platform
RNA libraries were prepared for sequencing using standard Illumina protocols for Illumina HiSeq4000 platform

value: adipocyte-specific SMRT knockout (adSMRT-/-)

value: 20 weeks

value: whole perigonadal adipose tissue


title: KNOCKOUT 3


title: Tumor1_Pt-344

description:
Sample name: NY2202
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-462

description:
Sample name: NY2133
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-357

description:
Sample name: NY2101
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-448

description:
Sample name: NY2088
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: KNOCKOUT 2


title: Tumor2_Pt-186

description:
Sample name: NY2064
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-448

description:
Sample name: NY2087
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: KNOCKOUT 1


title: Tumor1_Pt-186

description:
Sample name: NY2063
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-356

description:
Sample name: NY2029
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-356

description:
Sample name: NY2028
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-458

description:
Sample name: NY2167
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: WILDTYPE 3

source_name: wild type_adipose tissue

value: wild type


title: Tumor3_Pt-215

description:
Sample name: NY2013
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-462

description:
Sample name: NY2134
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor2_Pt-215

description:
Sample name: NY2012
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: Tumor1_Pt-215

description:
Sample name: NY2011
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: WILDTYPE 2


title: Tumor2_Pt-457

description:
Sample name: NY2007
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: WILDTYPE 1


title: Tumor1_Pt-457

description:
Sample name: NY2006
Genomic DNA extracted from multinodular HCC cases was genotyped with HumanOmniExpress-12v1 BeadChip (Illumina).


title: ΔmotB rep 3

city: Bloomington

first: Yves

middle: V

last: Brun

state: IN

address: 1001 E Third Street

department: Biology

institute: Indiana University

data_processing:
Read sequences were de-multiplexed using bcl2fastq (software v2.20.0.422)
Trimmomatic (version 0.33) was used to trim reads of adapter and low-quality bases
Reads were mapped to Caulobacter crescentus NA1000 (NC_011916.1) with bowtie2
Read counts were assigned to genes and intergenic features using a custom PERL script
Differential comparisons of all features with 5 or more reads were carried out with DESeq2 (R package version 3.4.0)
Genome_build: Caulobacter crescentus NA1000 (NC_011916.1)
Supplementary_files_format_and_content: Tab-delimited counts file indicating how many reads were mapped to each genomic entity

organism: Caulobacter vibrioides NA1000

source_name: cells

extract_protocol:
RNA was extracted using the RNA Isolate II kit (Bioline) and treated with DNase I. RNA was then purified using Rneasy MinElute Cleanup kit (Qiagen), and then treated with Ribo-Zero rRNA (Bacteria) removal kit (Illumina)
Purified RNA was prepared using TruSeq Stranded mRNA HT Sample Prep kit (Illumina) according to manufacturer's protocols; dual-indexed adapters were added to libraries for multiplexing and then libraries were cleaned by AMPure XP beads (Beckman Coulter)

value: {delta}motB

tag: molecule subtype

value: fragmented rRNA depleted RNA TEX treated


title: ΔmotB rep 2


title: 7-sp-C4

first: Yanxia

last: Gao

address: No. 800, Dongchuan Road

institute: Shanghai Jiaotong University

description:
processed data file: All_Differentially_Expressed_Genes.xlsx
processed data file: All_Differentially_Expressed_Transcripts.xlsx

data_processing:
Sequence quality was examined using the FastQC software.
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software (v2.0.4).
The transcript abundances for each sample was estimated with StringTie (v1.2.3), and the FPKM value for gene and transcript level were calculated with R package Ballgown(v2.6.0).
The differentially expressed genes and transcripts were filtered using R package Ballgown.
The novel genes and transcripts were predicted from assembled results by comparing to the reference annotation using StringTie and Ballgown.
Genome_build: Reference genome mm10 (GRCm38)
Supplementary_files_format_and_content: All_Differentially_Expressed_Genes.xlsx: Excel file
Supplementary_files_format_and_content: All_Differentially_Expressed_Transcripts.xlsx: Excel file

source_name: brain

extract_protocol:
ARC tissues in the coronal brain sections were accurately cut with syringe needles under the microscope and homogenized immediately in the TRIZOL reagent (Invitrogen). Total RNA was separated using chloroform and precipitated with isopropanol.
1~2 μg total RNA was used to prepare the sequencing library in the following steps: 1) Total RNA is enriched by oligo(dT) magnetic beads (rRNA removed); 2) RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific. The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification qPCR method. To sequence the libraries on the Illumina HiSeq 4000 instrument, the barcoded libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified in situ, and subsequently sequenced for 150 cycles for both ends on Illumina HiSeq instrument.

tag: strain/background

tag: gender

value: female

value: 4 months

value: arcuate nucleus


title: ΔmotB rep 1


title: 7-sp-C2


title: ΔflgE rep 3

value: {delta}flgE


title: WT rep 3


title: WT rep 2


title: 7-sp-1


title: ΔflgE rep 2


title: WT rep 1


title: ΔflgE rep 1


title: Male_BWm_Liver_biological replicate 2

city: New York City

first: Dimitris

last: Nasias

state: New York

address: 550 1st Avenue

department: Langone Medical School

institute: New York University

hyb_protocol: labelled cDNA was hybridized overnight to GeneChip™ Mouse Gene 2.0 ST Affymetrix expression arrays.

scan_protocol: GeneChip® Scanner 3000 7G (Affymetrix/ThermoFisher Scientific)

data_processing:
Affymetrix Expression Console Software Version 1.4.1.46 was used for the normalization, summarization and quality control of the microarray data. Affymetrix® Transcriptome Analysis Console (TAC) Software (Version 3.1.0.5) was used for the determination of the differentially expressed genes by performing p-value and fold change thresholds (One Way Analysis of Variance (One-Way ANOVA): p-value <0.05 and absolute fold change >1.5).
The sample data table summarizes the normalized expression values of each sample in log2 scale for all the probe sets. Data derive from the analysis in Affymetrix Expression Console Software Version 1.4.1.46.

label_protocol: The aRNA was purified, reverse transcribed and the resulting cDNA was fragmented, labelled following standard Affymetric protocol

growth_protocol: All experiments were performed with 9-12 weeks old male ApoE3L.CETP mice obtained from TNO (TNO, Innovation for Life, The Hague, The Netherlands). After a period of 2 weeks to acclimate, mice were switched to a high fat and high cholesterol diet (HFDC) diet containing 60% fat and 0.25% cholesterol (D14010701, HFDC, Research Diets, New Brunswick NJ, USA) for 6 weeks prior to RYGB or Sham surgery. Animal experiments were approved by the Cantonal Veterinary Office of Zurich (license 122/2014). All animals were euthanized by cardiac puncture 20 days after surgery.

extract_protocol: PureLink® RNA Mini Kit (ThermoFisher Scientific) was used for RNA isolation according to the manufacturer's instructions. Sample processing was performed using the GeneChip WT PLUS Reagent Kit (Affymetrix/ThermoFisher Scientific).Starting from total RNA, first and second strand cDNA synthesis was performed. The double stranded cDNA was transcribed to aRNA (amplified RNA) during in vitro transcription (IVT).

treatment_protocol: Mice were allocated to RYGB or Sham surgery according to their body weight. Mice were single housed after surgery. Body weight was measured weekly prior to surgery and daily after surgery. Daily food intake was measured manually, 4h prior to dark onset and expressed as grams/day consumed. The same cohorts of mice underwent oral glucose tolerance (OGTT) and insulin sensitivity (IST) tests. Before surgery, the tests were performed when mice were fed chow diet (11-14 weeks of age) and after the switch to HFDC diet at 17-20 weeks of age. OGTTs and ISTs were repeated 13 and 19 days after surgery, respectively, with seven days of recovery in between.

value: 9-12 weeks

tag: Sex

value: male

tag: sample group

value: body weight-matched (BWm)

value: liver


title: 7-sp-2

description:
The R2 raw data file is not available.
processed data file: All_Differentially_Expressed_Genes.xlsx
processed data file: All_Differentially_Expressed_Transcripts.xlsx

tag: age


title: Male_BWm_Liver_biological replicate 3


title: 17-92-C2


title: Mammary epithelial cells, NaAc & BHBA3

city: Harbin

first: Xiaoming

state: Heilongjiang

address: 600 changjiang road

institute: northeast agricultural university

data_processing:
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FPKM) method. RNA-Seq by Expectation-Maximization was used to quantify gene abundances
DESeq2 was used to identify significantly differentially expressed genes between high-milk-fat and control groups. P values were corrected for multiple testing using the method of Benjamini and Hochberg. Genes that had a corrected p < 0.05 were considered to be differentially expressed.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: FPKMs

organism: Bos taurus

source_name: Mammary gland

extract_protocol:
Total RNA was isolated using the Magen HiPure Total RNA Mini Kit (Magen, Guangzhou, China). RNA concentration was measured using a NanoDrop 2000 (Thermo Scientific, Wilmington, DE) and RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). All samples used in this study had an RNA integrity number > 8 (Supplementary Table S2). Six individual libraries were constructed: three from high-milk-fat samples and three from control samples.
RNA-seq transcriptome libraries were prepared following the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA) using 5 μg of total RNA. mRNA was isolated according to standard poly(A) selection methods using oligo (dT) beads and then fragmented in fragmentation buffer. cDNA was synthesized using a SuperScript Double-stranded cDNA Synthesis Kit (Invitrogen) with random hexamer primers (Illumina). Synthesized cDNA was subjected to end repair, phosphorylation, and A-base addition. Libraries were size-selected for cDNA target fragments of ~200-300 bp on 2% low-range ultra agarose and then amplified followed by 15 cycles of PCR. After quantification on a TBS380 fluorometer (American Instrument Exchange, Inc., Haverhill, MA), paired-end RNA-seq sequencing libraries were sequenced on an Illumina HiSeq 4000 (2 × 150-bp read length)

tag: species

value: Bos taurus

tag: cell

value: mammary epithelial cells

tag: treatment

value: acetate and BHBA addition


title: Male_Sham_Liver_biological replicate 4

tag: genotype/variation

value: Sham surgery


title: Male_BWm_Liver_biological replicate 1


title: Male_Sham_Liver_biological replicate 3


title: Male_Sham_Liver_biological replicate 2


title: Mammary epithelial cells, NaAc & BHBA2


title: Male_BWm_Liver_biological replicate 4


title: Male_Sham_Liver_biological replicate 5


title: Mammary epithelial cells, Control3

value: Control


title: 17-92-C1


title: 17-92-2


title: Mammary epithelial cells, NaAc & BHBA1


title: Mammary epithelial cells, Control2


title: Mammary epithelial cells, Control1


title: 17-92-1


title: Male_Sham_Liver_biological replicate 1


title: sHCC-Pt3

value: Tumor

value: FFPE


title: Dminus

city: Dublin

first: Thomas

last: Hall

state: Select One

address: 2, Taney Grove

department: Vet sciences

country: Ireland

institute: UCD

data_processing:
At each step of data processing, read quality was assessed via fastqc version 0.11.5
Sequenced reads were trimmed for adaptor sequence and the raw reads were aligned to the most recent build of the UMD 3.1.1 bovine transcriptome via salmon (version 0.8.1)
Aligned reads were also counted in Salmon and the resulting quantification files were annotated at gene level via tximport (version 3.7)
Genome_build: UMD 3.1
Supplementary_files_format_and_content: Plain text, tab seperated quantification file denoting Name of sequence, Length, Effective Length, TPMs and the number of reads aligned

growth_protocol: Centrifuged cell pellet was resuspended in 15 ml of R10+ media and placed in a 75 cm [2] vented culture flask (CELLSTAR®, Greiner Bio-One Ltd., Stonehouse, UK) and incubated for 24 h at 37 °C, 5% CO2. After incubation, media was removed together with non-adherent cells and adherent cells were washed with 15 ml HBSS pre-warmed to 37 °C (Note: all pre-warmed media and solutions were heated to 37 °C prior to use). Adherent cells were dissociated by adding 10 ml pre-warmed 1× non-enzymatic cell dissociation solution (Sigma–Aldrich Ltd.) to each culture flask and incubating at room temperature for 10 min. Cells were then pelleted (200× g for 5 min at room temperature), resuspended in 10 ml pre-warmed R10+ media and the number of viable cells was counted using a Beckman Coulter® Vi-CELL™ XR Cell Viability Analyzer and reagent kit (Beckman Coulter Inc., High Wycombe, UK).

extract_protocol: RNA was extracted from infected (n = 4) and control (n = 4) bAM samples using the RNeasy Plus Mini Kit (Qiagen) as previously outlined (10.1095/biolreprod.111.094946). All RNA samples were of excellent quality (RIN >9).

treatment_protocol: 2 x 10^6 macrophages were seeded in 60 mm tissue culture plates and challenged with M. bovis at an MOI of 10:1 (2 X 107 bacteria per plate) for 24 hours, parallel non-infected controls were prepared simultaneously.

tag: animal

value: Animal 4

tag: condition

tag: timepoint

value: 24 HPI

tag: cell type

value: Bovine alveolar macrophages


title: Cminus

value: Animal 3


title: Dplus

value: Infected


title: Cplus


title: EPC_GEO

city: San Diego

first: Oscar

middle: E

last: Echeagaray

state: CA

address: 5500 Campanile Drive

institute: San Diego State University

data_processing:
The raw data was processed with the Cell Ranger pipeline (10X Genomics; version 2.0). Reads were aligned to the Homo sapiens hg19 genome.
Preparations derived from in vitro studies, yielded 5659 barcoded cells for analysis, from which 1125, 1717, 1403 and 1414 corresponded to CardioClusters, CPC, EPC and MSCs. Cells with less than 1000 genes or more than 10% of mitochondrial gene UMI count were filtered out and genes detected less than in three cells were filtered out. Approximately 2,029 variable genes were selected based on their expression and kept for downstream analysis using Seurat R Package (v2.3.4).
Sequenced reads were aligned to the human reference genome hg19
Genome_build: hg19
Supplementary_files_format_and_content: comma separated values of digital expression matrix; rows are genes; columns are cells with cell barcode

source_name: EPC

extract_protocol:
Fatty tissue was excised and remaining cardiac tissue was suspended in Basic Buffer (15 mL) and minced into 1 mm3 pieces. After mincing, tissue and Basic Buffer were collected in 50 mL Falcon tube. Digestive solution containing collagenase, type II 225 U/mg dry weight (Worthington, catalog #LS004174, Bio Corp, Lakewood, NJ) was dissolved in Basic Buffer (2-2.5 mg/mL) and incubated with tissue pieces for 1.5-2 hours at 37°C with continuous shaking. Digestion solution was refreshed at the one-hour time point and resulting suspensions were centrifuged at 350 g and resuspended in CPC media. Final suspension was filtered through a 100-µm filter (Corning, Inc., catalog #352360) followed by a 40-µm filter (Corning, Inc., catalog #352340) and centrifuged at 150 g for 2 minutes to collect CMs. The supernatant was collected and centrifuged at 350 g and resuspended in CPC media and incubated overnight at 37°C in 5% CO2 incubator. The following day, cells in suspension were collected in 50 mL Falcon tube. Any cells attached were dissociated using a 1:1 mixture of Cellstripper (Corning, catalog #25-056-CI) and TrypLE Express (1X) (Thermo Fisher Scientific, catalog #12604-013). Resulting suspension was filtered through a 40-µm filter, centrifuged at 350 g, and resuspended in wash buffer (PBS plus 0.5% bovine serum albumin). To isolate c-Kit+ cells, suspension was incubated with c-Kit–labeled beads (Miltenyi Biotec, catalog #130-091-332) and sorted according to the manufacturer’s protocol. The c-Kit+ fraction was divided as such: half the population was suspended in CPC media and the other half was suspended in EPC media. To isolate an EPC population, at 1 week the c-Kit+ population plated in EPC media was further sorted using CD133–labeled beads and sorted according to the manufacturer’s protocol (Miltenyi Biotec, catalog #130-097-049). All cells were cultured at 37°C in 5% CO2 incubator in their respective growth media. CPC and EPC were split 1:2 when they reached 60-70% confluency. MSC were split 1:2 when they reached 90% confluency. All cells used in this study were mid-passage (passages 5–10).
The Chromium Single Cell 3' Library & Gel Bead Kit v2 (PN- 120237), Chromium Single Cell 3' Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used according to the manufacturers instructions in the Chromium Single Cell 3' Reagents Kits V2 User Guide.

value: endothelial progenitor cells (EPC)

tag: cell subtype


title: CardioCluster_GEO

source_name: CardioCluster

value: CardioCluste

value: CPC, MSC and EPC cultured in 3D


title: Tumor2_Pt-461_gene_expression

description:
Sample name: NY2199
RNA extracted from multinodular HCC cases was analyzed with HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina)

value: HCC tissue from cirrotic liver

tag: pathologic classification

tag: tissue preparation


title: Bplus

value: Animal 2


title: CPC_GEO

source_name: CPC

value: cardiac progenitor cells (CPC)

value: cKit +


title: Bminus


title: A2-MB-PolII

description: batch number: 0212_BHJ77HBBXX

data_processing:
At each step of data processing, read quality was assessed via fastqc version 0.11.5
ChIP-seq reads aligned to bovine reference genome via Bowtie2 version 2.3.0
All resulting SAM files converted  into sorted BAM files via Samtools (version 1.3.1)
The peak calling was carried out via macs (version 2.1.1.20160309), normalised by input samples. Broadpeak or narrowpeak calls based on mark. Peaks filtered based on pvalue < 0.05 and fold enrichment > 2.5
BEDgraph files generated via MACS2 and compared via MACS2 bdgcmp
Genome_build: UMD 3.1
Supplementary_files_format_and_content: BEDgraph converted to bigwig via bedtools

source_name: MB-PolII

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
NEB Next Ultra ChIPseq Library Prep (New England Biolabs) for ChIP-seq library preparations.

tag: animal id

tag: chip antibody

value: PolII

tag: chip antibody vendor

value: Santa-cruz

tag: chip antibody cat. #


title: A2-MB-K27me3

description: batch number: 0212_BHJ77HBBXX

value: Millipore


title: Aplus

value: Animal 1


title: PHF7-flag-ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 1.2 with the following configurations: -m 1 -X 500
Only uniquely aglined reads are kept for downstream analysis.
Peaks were called using MACS 1.3.7.1 with defalut parameters
Genome_build: mm9
Supplementary_files_format_and_content: Scores in bigwig files  represent the reads per kilobase per million reads (RPKM).

source_name: late spermatids from Phf7-flag mice

growth_protocol: Late spermatids isolated from testes of Phf7-flag mice according to reported protocol (Bastos et al., 2005)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: spermatid

tag: strain

value: C57BL/6 (Flag-g4)


title: PHF7-flag-input

tag: age


title: Male_Rygb_Liver_biological replicate 6

value: 9-12 weeks

tag: Sex

value: male

tag: sample group

value: Roux-en-Y gastric bypass (RYGB) surgery

tag: tissue

value: liver


title: Male_Rygb_Liver_biological replicate 4

tag: genotype/variation


title: A2-CTRL-input

description: batch number: 0212_BHJ77HBBXX

source_name: CTRL-input

value: Control

value: Bovine alveolar macrophages


title: A2-CTRL-K27me3

description: batch number: 0212_BHJ77HBBXX


title: A2-CTRL-K4me3

description: batch number: 0212_BHJ77HBBXX


title: MSC_GEO

source_name: MSC

value: mesenchymal stem cells (MSCs)


title: A2-CTRL-PolII

description: batch number: 0212_BHJ77HBBXX

source_name: CTRL-PolII


title: A2-MB-K4me3

description: batch number: 0212_BHJ77HBBXX

value: Infected


title: ub-H2A-input

value: C57BL/6 (Flag-d2)


title: A1-MB-K27me3

description: batch number: 0212_BHJ77HBBXX


title: Male_Rygb_Liver_biological replicate 2


title: Male_Rygb_Liver_biological replicate 3


title: A1-MB-PolII

description: batch number: 0212_BHJ77HBBXX


title: Aminus

tag: animal

value: 24 HPI


title: A1-CTRL-PolII

description: batch number: 0212_BHJ77HBBXX

tag: condition


title: A1-MB-K4me3

description: batch number: 0212_BHJ77HBBXX


title: Male_Rygb_Liver_biological replicate 1


title: Cirrh-Pt42

description:
Sample name: NY5236
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

data_processing: Genotype, Log R ratio (LRR, reflecting total copy number) and B-allele frequency (BAF) obtained from GenomeStudio were used for CNV detection.

source_name: Non-tumor cirrhotic liver

extract_protocol: Genomic DNA was extracted from seven to ten macrodissected FFPE sections (5 μm) using the automated procedure QIAcube and QIAGEN spin columns (Qiagen, Hilden, Germany). For fresh-frozen samples, tissues were processed for gDNA extraction using the Invitrogen ChargeSwitch genomic DNA Mini Tissue.

value: Non-tumor cirrhotic liver

value: Cirrhosis

tag: pathologic subclassification

value: Cirrhotic

value: FFPE


title: H3K4me3-ChIP-seq

tag: cell type

value: H3K4me3(Active motif,39916)


title: ub-H2A-ChIP-seq

value: spermatid


title: A1-CTRL-K27me3

description: batch number: 0212_BHJ77HBBXX

value: Animal 1

value: Millipore


title: Cirrh-Pt53

description:
Sample name: NY644
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt38

description:
Sample name: NY5228
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt45

description:
Sample name: NY5244
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt32

description:
Sample name: NY5214
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: H3K4me3-input


title: Cirrh-Pt30

description:
Sample name: NY5210
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt28

description:
Sample name: NY5206
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt49

description:
Sample name: NY5252
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: N4_CD8_TGF

city: Montreal

first: Jean-Sebastien

last: Delisle

state: Quebec

address: 5415, boulevard de l’Assomption

country: Canada

institute: Centre de recherche de l’Hôpital Maisonneuve-Rosemont

description:
CD8_rawcounts.txt
CD8_normalized.txt

data_processing:
Global gene expression profiles were performed on an Ion Proton sequencer using the Ion Ampliseq Transcriptome Human Gene Expression Kit.
Each sample was sequenced and aligned using the Torrent Suite software v5.0.5. Raw readcounts were generated by the ampliSeqRNA plugins.
The data were analyzed using Bioconductor packages and R statistical language. Differentially expressed genes analysis was performed using the DESeq2 package version 1.6.3 with raw readcounts from AmpliSeq. Read count normalization was performed using the regularized logarithm (rlog) method provided in DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include rawcounts and normalized values for each sample.

source_name: CD8 T cells

growth_protocol: T cells were enriched from peripheral blood mononuclear cells by the Human T cell enrichment kit (StemCell Technologies). A total of 1 x 10^5 T cells were stimulated in 96-well U-bottom culture plates with 5 µg/ml plate-bound anti-CD3e and 1 µg/ml soluble anti-CD28, in T-cell media (Advanced RPMI 1640, 10% human serum and 1X L-glutamine) with Penicillin-Streptomycin Solution at 37oC and 5% CO2.

extract_protocol:
T cells were FACS-sorted with an Aria III instrument into CD4 and CD8 subsets. RNA was extracted with Qiagen RNeasy mini kit.
cDNA was amplified using the Ion Ampliseq Transcriptome Human Gene Expression Core Panel (targeting 20812 RefSeq genes). 16 libraries were generated and barcoded using Ion Xpress Barcode Adapters 1-16 kit, combined together to generate polls of 8 samples, loaded on the Ion Chef instrument for template preparation and loading on Ion P1 v3 chips.

treatment_protocol: 5 ng/ml of recombinant human TGF-β

value: T cells

tag: harvest time

value: 7 days of culture

tag: treatment

value: 5 ng/ml of recombinant human TGF-β


title: Cirrh-Pt109

description:
Sample name: B294
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

tag: pathologic classification

tag: tissue preparation

value: FFz


title: Cirrh-Pt40

description:
Sample name: NY5232A1
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt52

description:
Sample name: NY600
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: WILDTYPE 4

value: wild type

value: 20 weeks

value: whole perigonadal adipose tissue


title: Ross Rep 2

city: Ahvaz

first: Seyed

middle: Nader

last: Albooshoke

state: khozestan

address: sazeman aab-o-bargh

department: Animal Science

country: Iran

institute: Khuzestan Agricultural and Natural Resources Research and Education Center

description: Results of sequencing.xlsx

data_processing:
Quality checks were performed on a raw sequence data using FastQC (version 0.11.5). To remove the low quality paired-end reads as well as reads containing adapter sequences, Trimmomatic (current version 0.36, http://www.usadellab.org/cms/?page=trimmomatic) was run on each sample, using its adaptive trimming algorithm MAXINFO with a target length of 50 and strictness of 0.9. The clean reads were then reanalyzed with FastQC to confirm the quality improvements.
Paired-end reads from each sample that passed the quality filters were aligned to the reference Galgal5 genome using Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT2) v2.0.4.)
Aligned reads were then assembled into transcripts using Cufflinks version 2.2.1, guided by Ensembl annotation, to construct and identify both known and novel transcripts
Here, abundances of transcripts were upper-quartile normalized to account for differences in library sizes and also, the genome reference sequence was applied for sequence bias correction in order to improve expression estimates. The expression level of each transcript was estimated as Fragments Per Kilo base per Million mapped reads
Genome_build: The Galgal5 reference genome and the annotation GTF file for chicken (release 89)

organism: Gallus gallus

source_name: Breast muscle

extract_protocol:
The extraction of total RNA from each muscle sample was performed using Trizol reagent (Invitrogen, USA), following the manufacturers protocol. The purity and concentration of RNA were detected by NanoDrop (Thermo Scientific™ NanoDrop 2000) and gel electrophoresis, respectively. The 28S/18S ratio for RNA samples ranged from 1.8 to 2. cDNA libraries were constructed using the TruSeq® RNA Sample Preparation Kit v2 (Illumina®, USA) and deep sequenced by the BGI Company (China, Shenzhen).
Three RNA samples from the same breed were pooled (by mixing together equal quantities of RNA) to generate a total of 4 pooled RNA samples (two samples in each breed). An Illumina® HiSeq™ 2000 sequencer was used to sequence the libraries, according to the manufacturer’s instructions, so as to generate paired-end reads of 150 base pair.

value: Pectoralis muscle

value: day 28 post-hatch

tag: breed

value: Ross 708 broilers


title: Ross Rep 1

description: Results of sequencing.xlsx


title: Cirrh-Pt43

description:
Sample name: NY5238
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: Non-tumor cirrhotic liver

value: Cirrhosis


title: Isfahani Rep 1

description: Results of sequencing.xlsx

value: Isfahani's native chickens


title: Isfahani Rep 2

description: Results of sequencing.xlsx


title: A1-CTRL-input

description: batch number: 0212_BHJ77HBBXX

tag: animal id

value: Control

value: Bovine alveolar macrophages

tag: chip antibody


title: N3_CD8_TGF

description:
CD8_rawcounts.txt
CD8_normalized.txt


title: Cirrh-Pt22

description:
Sample name: NY843
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: Cirrhotic

value: FFPE


title: Cirrh1-Pt33

description:
Sample name: NY5216
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt19

description:
Sample name: NY837
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt18

description:
Sample name: NY835
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt10

description:
Sample name: NY819
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt15

description:
Sample name: NY829
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: N2_CD8_TGF

description:
CD8_rawcounts.txt
CD8_normalized.txt

value: T cells


title: N4_CD8

description:
CD8_rawcounts.txt
CD8_normalized.txt

value: 7 days of culture

value: Untreated


title: N3_CD8

description:
CD8_rawcounts.txt
CD8_normalized.txt


title: Cirrh-Pt9

description:
Sample name: NY817
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt8

description:
Sample name: NY815
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt29

description:
Sample name: NY5208
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt2

description:
Sample name: NY803
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt4

description:
Sample name: NY807
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: N2_CD8

description:
CD8_rawcounts.txt
CD8_normalized.txt


title: N4_CD4_TGF

description:
CD4_rawcounts.txt
CD4_normalized.txt

source_name: CD4 T cells

value: 5 ng/ml of recombinant human TGF-β


title: Cirrh-Pt1

description:
Sample name: NY801
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt23

description:
Sample name: NY845
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt21

description:
Sample name: NY841
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt20

description:
Sample name: NY839
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt24

description:
Sample name: NY847
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: N3_CD4_TGF

description:
CD4_rawcounts.txt
CD4_normalized.txt


title: A1-CTRL-K4me3

description: batch number: 0212_BHJ77HBBXX

value: Animal 1

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: N1_CD8_TGF

description:
CD8_rawcounts.txt
CD8_normalized.txt


title: Cirrh-Pt11

description:
Sample name: NY821
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt14

description:
Sample name: NY827
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt82

description:
Sample name: NY90
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: FFz


title: N2_CD4_TGF

description:
CD4_rawcounts.txt
CD4_normalized.txt


title: Cirrh-Pt80

description:
Sample name: NY71
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: N1_CD4_TGF

description:
CD4_rawcounts.txt
CD4_normalized.txt


title: N4_CD4

description:
CD4_rawcounts.txt
CD4_normalized.txt


title: Cirrh-Pt79

description:
Sample name: NY64
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh2-Pt33

description:
Sample name: NY5242
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt77

description:
Sample name: NY47
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: sHCC-Pt110

description:
Sample name: M271
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

source_name: HCC tissue from cirrotic liver

value: HCC tissue from cirrotic liver

value: sHCC

value: eHCC


title: sHCC-Pt43

description:
Sample name: NY5237
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Male_Rygb_Liver_biological replicate 5

tag: age

value: 9-12 weeks

tag: Sex

value: male

value: Roux-en-Y gastric bypass (RYGB) surgery

value: liver


title: sHCC2-Pt33

description:
Sample name: NY5241
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

tag: tissue


title: sHCC-Pt38

description:
Sample name: NY5227
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: sHCC-Pt30

description:
Sample name: NY5209
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: sHCC-Pt28

description:
Sample name: NY5205
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: sHCC-Pt32

description:
Sample name: NY5213
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: sHCC-Pt109

description:
Sample name: B295
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: veHCC


title: sHCC-Pt52

description:
Sample name: NY599
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: sHCC1-Pt33

description:
Sample name: NY5215
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: sHCC-Pt40

description:
Sample name: NY5231
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: sHCC-Pt49

description:
Sample name: NY5251
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: sHCC-Pt29

description:
Sample name: NY5207
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Cirrh-Pt75

description:
Sample name: NY17
Genomic DNA extracted from non-tumoral cirrhotic tissue was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: Non-tumor cirrhotic liver

value: Cirrhosis

value: Cirrhotic


title: sHCC-Pt125

description:
Sample name: M371
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: N3_CD4

description:
CD4_rawcounts.txt
CD4_normalized.txt

value: T cells

value: 7 days of culture


title: sHCC-Pt53

description:
Sample name: NY643
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: FFPE


title: Dysplastic5-Pt79

description:
Sample name: NY53
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

source_name: Pre-malignant dysplastic nodule from cirrotic liver

value: DN

value: HGDN


title: sHCC-Pt45

description:
Sample name: NY5243
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Dysplastic-Pt76

description:
Sample name: NY29
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: Pre-malignant dysplastic nodule from cirrotic liver

value: FFz


title: N2_CD4

description:
CD4_rawcounts.txt
CD4_normalized.txt

value: Untreated


title: sHCC-Pt42

description:
Sample name: NY5235
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: HCC tissue from cirrotic liver

value: sHCC

value: eHCC


title: Dysplastic2-Pt75

description:
Sample name: NY15
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Dysplastic-Pt24

description:
Sample name: NY846
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Media comparison, replicate 2

city: Neuherberg

first: Fatma

last: Uzbas

address: Ingolstaedter Landstr. 1

department: Institute of Stem Cell Research

institute: Helmholtz Center Munich

description:
custom fa file:
Barcodes_MediumComparison.fa
Amplicons_Pluripotency.fa

data_processing:
FASTQ files from sequencing run were processed  to assign the reads to barcode combinations and amplicons, using the demultiplexing pipeline provided with the BART-Seq method.
Genome_build: Custom reference consisting of target amplicon sequences
Supplementary_files_format_and_content: Count matrices (*.csv) contain the processed read counts assigned to each forward × reverse barcode combination per amplicon. Fasta files (*.fa) contain the Barcode and Amplicon sequences used for demultiplexing.

source_name: Single/multiple H9 hESCs and BJ fibroblasts

extract_protocol:
Bulk RNA was extracted from HMGU1/H9 cells using Qiagen RNeasy Mini Kit. Single/multiple cells are FACS-sorted directly into the reverse transcription reaction mixture and lyzed by a freeze-thaw cycle (RNA was not purified).
Adapted protocol from NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (provided with the BART-Seq method)

tag: cell lines

value: H9 hESCs, BJ fibroblasts

tag: growth media

value: hESCs:mTeSR™1 / KSR-bFGF / E8; fibroblasts:DMEM-based

tag: primer concentration

value: 0.75 uM in PCR

tag: range of sorted cells per well


title: Dysplastic-Pt22

description:
Sample name: NY842
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

tag: pathologic subclassification


title: Dysplastic-Pt19

description:
Sample name: NY836
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Media comparison, replicate 1


title: Dysplastic-Pt18

description:
Sample name: NY834
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Dysplastic-Pt15

description:
Sample name: NY828
Genomic DNA extracted from dysplastic nodules or small hepatocellular carcinomas was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).


title: Hela cells transfected with siTHOC1 for 72 h, biological rep1

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

description: Gene expression from HeLa cells after 72 h of siTHOC1 transfection

hyb_protocol: Following fragmentation, 5.2 µg of ss-cDNA were hybridized for 16 h at 45 ºC on GeneChipTM Human Transcriptome (HTA) Array 2.0 . GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G and the images were acquired by Affymetrix GeneChip Comand Console®  (AGCC) Software.

data_processing:
The .CEL files generated with AGCC software were processed and normalized  into expression values using the SST (Signal Space transformation)-RMA (Robust Microarray Average) method by Expression Console (Affymetrix). The following gene level and alternative splicing analysis (ANOVA unpaired one-way) were performed using the Transcriptome Analysis Console (TAC) Software developed by Affymetrix.
affymetrix-algorithm-name = 'sst-rma-gene-full' -or- 'sst-rma-alt-splice: sst-dabg'
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: THOC1-depleted HeLa cells

label_protocol: Total RNA from each sample (100 ng) was used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip WT PLUS Reagent Kit User Manual (Affymetrix)

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; GIBCO, Thermo Scientific, Waltham, MA) supplemented with 10% heat-inactivated fetal bovine serum at 37°C (5% CO2). ON-TARGETplus Non-targeting Pool (control siRNA) and ON-TARGETplus SMARTpool human MFAP1 and human THOC1 from Dharmacon were used for depletions. Transient transfection of siRNA was performed using DharmaFECT 1 (Dharmacon) according to the manufacturer’s instructions. Assays were performed 72 h after siRNA transfection.

extract_protocol: Total RNA was isolated from HeLa cells transfected with siRNA for 72 h using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

tag: cell line

value: HeLa

tag: sirna transfection

value: siTHOC1 for 72 h