title: Corrected sample 2

city: Helsinki

first: Diego

last: Balboa

address: Biomedicum 1, Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
Data were processed with previously published Python scripts (doi:10.1016/j.cell.2015.04.044; doi:10.1038/nprot.2016.154).
Transcript reads were trimmed with Trimmomatic 0.36 (arguments: LEADING:28, SLIDINGWINDOW:4:20, MINLEN:16), and barcode reads were filtered for expected structure (known cellular barcode, W1 adapter sequence, poly-T tail).  A Hamming distance threshold of 5 was used for for W1 sequence matching and a minimum poly-T length of 3.
The filtered reads were sorted based on barcodes, and barcodes having at least 20 000 reads were kept.  The filtered reads were aligned with bowtie 1.1.1 (arguments: -a --strata --best --norc --sam -m 200 -n 1 -l 15 -e 80) to the Ensembl GRCh38.85 cDNA reference from which haplotypic transcripts were removed. A poly-A sequence of 125 bases was added to each transcript before building the bowtie index.
UMI quantification was performed with the previously published scripts using the following arguments: m : 10, u : 1, d : 600, split-ambigs : False, mixed_ref : False, min_non_polyA : 10.
See the supplementary materials of the publication for the scripts used.
Genome_build: GRCh38
Supplementary_files_format_and_content: A text file containing a UMI count matrix with genes as rows and cells as columns. The first three columns are per-gene summaries for total and ambiguous counts.

source_name: iPSC-derived pancreatic islet-like aggregates

growth_protocol: iPSC cells were dissociated with 5 mM EDTA treatment for 10 min and seeded at 1.5-2 million cells/3.5 cm well on Matrigel-coated plates with E8 medium containing 5 μM ROCK inhibitor (Y-27632 2HCl, Selleckchem). Differentiation was started 24 h later and proceeded through 7 stages differentiation protocol (Stages 1 to 4 in adherent culture and stages 5 to 7 in suspension culture):   - Definitive endoderm induction (3 days): cells were washed 1xPBS (without Ca2+/Mg2+) and 2 mL medium/3.5 cm well of differentiation media was applied: MCDB131 (10372-019, Life Technologies) + 2mM Glutmax (35050038, Life Technologies) + 1.5 g/L NaHCO3 (Sigma-Aldrich) + 0.5% BSA fraction V Fatty acid free (Sigma-Aldrich) + 10 mM final glucose (Sigma-Aldrich) + 100 ng/ml ActA + 3 μM CHIR. CHIR concentration was reduced to 0.3 μM and 0 μM on day 1 and day 2 respectively.  - Stage 2 posterior foregut induction (for 3 days, medium changed every day): MCDB131 + 2mM Glutmax + 1.5 g/L NaHCO3 + 0.5% BSA fV + 10 mM final glucose + 0.25 mM Ascorbic acid (A4544, Sigma-Aldrich) + 50 ng/mL FGF7 (Z03047, Genscript)  - Stage 3 pancreatic endoderm induction (for 2 days, medium changed every day): MCDB131 + 2mM Glutmax + 2.5 g/L NaHCO3 + 2% BSA fV + 10 mM final glucose + 0.25 mM Ascorbic acid + 50 ng/mL FGF7 + 0.25 μM SANT1 (S4572, Sigma-Aldrich) + 1 μM RA + 100 nM LDN + 1:200 ITS-X (51500-056, Life Technologies) + 200 nM TPB (sc-204424, Santa Cruz).  - Stage 4 pancreatic progenitor induction (3 days, medium changed every day): MCDB131 + 2mM Glutmax + 2.5 g/L NaHCO3 + 2% BSA fV + 10 mM final glucose + 0.25 mM Ascorbic acid + 2 ng/mL FGF7 + 0.25 μM SANT1 + 0.1 μM RA + 200 nM LDN + 1:200 ITS-X + 100 ng/mL EGF (AF-100-15, Peprotech) + 10 mM Nicotinamide (N0636, Sigma-Aldrich).  - Stage 5 endocrine induction: Cells were washed 2x with EDTA, treated with TrypLE for 10 min at 37ºC, 1 mL/3.5 cm well. Cells were dissociated by pipetting, and spin down for 3 min at 200 rcf. Cells were resuspended in S5 medium with ROCK inhibitor at 10 uM, at a density of one million cells/mL, in a volume of 5 mL, in ultra-low attachment 6-well plates (3471, Corning) and placed in a rotating platform (InforsHT, Celltron) at 95 rpm in the incubator. After 24h, cells formed round aggregates and medium was changed to S5 without ROCK inhibitor: S5 medium (for 4 days, changed every day): MCDB131 + 2mM Glutmax + 1.5 g/L NaHCO3 + 2% BSA fV + 20 mM final Glucose + 1:200 ITS-X + 10 ug/mL Heparin (H3149, Sigma-Aldrich) + 0.25 μM SANT1 + 0.05 μM RA + 100 nM LDN + 10 μM ALK5inhII (S7233, Selleckchem) + 1 μM GC1 (4554, Tocris) + 10 μM Zinc Sulfate (Z0251, Sigma-Aldrich) + 20 ng/mL Betacellulin (100-50, Peprotech) + 100 nM GSiXX (565789, Millipore).  - Stage 6 media (14 days, change every second day): MCDB131 + 2mM Glutmax + 1.5 g/L NaHCO3 + 2% BSA fV + 20 mM final glucose + 1:200 ITS-X + 10 ug/mL Heparin + 100 nM LDN + 10 μM ALK5inhII + 1 μM GC1 + 100 nM GSiXX  + 10 μM Zinc Sulfate.  - Stage 7 media (7 days, change every second day): MCDB131 + 2mM Glutmax + 1.5 g/L NaHCO3 + 2% BSA fV + 20 mM final glucose + 1:200 ITS-X + 10 ug/mL Heparin + 10 μM ALK5inhII + 1 μM GC1 + 10 μM Trolox + 1 mM N-Acetylcysteine (A9165, Sigma-Aldrich) + 75 μM Resveratrol (R5010, Sigma-Aldrich) + 20 μM JNK inhibitor (SP600125, #1496, Tocris) + 2 μM R428 (S2841, Selleckchem).

extract_protocol:
Stage 7 islet-like aggregates were dissociated into single cells by incubation with a 1:1 mixture of TrypLE Express and Trypsin-EDTA for 10 min at 37ºC. Dissociated cells were passed through a 30 mm strainer to remove cell clumps.
Single cells were co-encapsulated into 3-4 nL droplets together with barcoded hydrogel beads and a mixture of reverse-transcription (RT) and lysis reagents. Within every single droplet, a cell was lysed and cDNA tagged with a barcode during reverse transcription. The droplet emulsion was broken and the bulk material was taken through the following steps: i) second strand synthesis; ii) linear amplification by in vitro transcription (IVT); amplified RNA fragmentation; iv) reverse transcription; v) PCR. The resulting DNA libraries were multiplexed and sequenced together on NextSeq Illumina platform in paired-end mode using a high-yield 75 cycle kit.

tag: cell type

value: Cells of stage 7 pancreatic islet-like aggregates differentiated from iPS cells

value: INS C96R corrected


title: GROUND BRIC A PDFU-2 332 WT

status: Public on Dec 01 2018

type: RNA

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

country: USA

institute: University of Florida

hyb_protocol: Amplified and labeled cDNA (5 µg/sample) was fragmented and hybridized with rotation onto Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays for 16h at 45°C. Arrays were washed on a Fluidics Station 450 (Affymetrix) with the Hybridization Wash and Stain Kit (Affymetrix) and the Washing Procedure FS450_0004.

scan_protocol: scan was performed using Affymetrix GeneChip Scanner 3000 7G

data_processing: The MAS5 data was generated by using the Affymetrix Expression Console software using default analysis settings and global scaling as normalization method.

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: wildtype_ground_control_solid media plates; BRIC-17; OES chamber: BRIC-A PDFU-2

label_protocol: cDNA was synthesized using Ovation Pico WTA System (NuGEN Technologies Inc.) and cDNA was labeled using Encore Biotin Module (NuGEN Technologies Inc.)

growth_protocol: General biology operations   Two Arabidopsis thaliana Col-0 cell culture lines were used: Wild Type (WT) and ARG1 KO SALK_024542C line (ARG1 T-DNA insertion knockout), all cell cultures derived from hypocotyls. Tissue culture cells were plated on 60mm round, nutrient agar Petri plates cultured in a horizontal position until turnover and installation into the BRIC hardware.  All of the sub-culturing on the plates was conducted in the laboratory of the PIs and the University of Florida.  Plates were planted in a laminar flow hood and stored in sterile Biotransfer Boxes (BT). Plates with cells were kept in the dark and at ambient temperature.  Preparation of specialized plates and biology  Petri plates.   Because of their configuration within the BRIC flight hardware, sterility was maintained on all surfaces (interior and exterior) of the Petri plates. The media in the plates for BRIC had to be 5mm deep or less to accommodate the biology and the PDFU cover hardware. For a 60mm dish, this calculates out to 6.7 mLs. After pouring, the plates are allowed to solidify, and then transferred to a sterile Biotransporter (to maintain sterility of external surface) until planting.  Preparation of cell culture plates.  The liquid media from a sterile cell suspension was decanted, and the cells were washed once with fresh liquid media, and then decanted again. A sterile scoop was used to place about 1 gram of cells in the surface on the plate and disperse evenly across the surface. The cover was replaced, but not taped, and transferred to a sterile BT.  The BT was wrapped in black cloth and stored at room temperature. The same day plates were transported by car to the Kennedy Space Center, NASA for the same night (3:00 AM) Turn Over. The ground control plates were turned over 48 hours later.   BRIC Spaceflight Hardware  The hardware for this experiment was the NASA BRIC-LED (Biological Research In a Canister – Light Emitting Diode). The LED component of the hardware was disabled and all biology was held in the dark for the duration of the experiment. The BRIC-LED canisters hold six 60 mm diameter Petri plates in small sub-compartments called PDFUs (Petri Dish Fixation Units). The PDFUs allow an externally activated fixation step without manipulating the samples. We were allocated 10 PDFUs: 5 in BRIC A and 5 in BRIC B. The 2 replicate plates of WT cultured cells and the 3 replicate plates of ARG1 KO were distributed among the BRIC A canister. The 2 replicate plates of WT cultured cells were distributed among the BRIC B canister. One of the PDFU slots in each BRIC was used to hold a HOBO™ data logger to record temperature. The HOBO temperature data collection begins immediately after the biology is sealed in the BRICs, 24 hours before launch.   An additional set of Petri plates within BRIC hardware, identical to that launched for Spaceflight, was prepared for the Ground Control. The Ground Control was housed in the OES (Orbital Environmental Simulator) chamber in the Spaceflight Life Sciences Laboratory (SLSL) at Kennedy Space Center (KSC). The Ground Control was initiated with a precise 24 hour delay to enable the OES environment to be programmed with the environmental profile taken from telemetry of the Space Shuttle. Nominally, the Ground Control BRIC hardware and samples experienced the same external environment profile as the hardware and samples on the Space Shuttle. Environmental parameters that are controlled on the OES and made identical to flight are cabin temperature, humidity and CO2 concentration.

extract_protocol: Total cellular RNA was extracted using RNeasy Mini Kit (QIAGEN)

treatment_protocol: The BRIC-17 experiment was turned over to payload engineers in the SLSL at KSC 48 hours before the scheduled launch time. The payload launched on Dragon cargo spacecraft, SpaceX CRS-2 on March 1st, 2013, at 10:10 EST, and achieved orbit approximately twelve minutes later. Dragon berthed to the ISS on the March 3rd, 2013. The biology was in orbit 10 days before being fixed on orbit with RNAlater. The Dragon unmanned spacecraft unberthed the ISS and splashed into Pacific on the March 26th and the biology was returned to the Kennedy Space Center and handed to the PIs at SLSL on the April the 2nd.

tag: flight status

value: ground control

tag: cultivar

tag: genotype

value: WT

tag: material type

value: Tissue culture cells

tag: tissue source

value: derived from hypocotyls of WT plant

tag: age

value: 14 days old

tag: biosource type

value: RNAlater fixed_sample


title: GROUND BRIC B PDFU-1 339 WT

source_name: wildtype_ground_control_solid media plates; BRIC-17; OES chamber: BRIC-B PDFU-1


title: GROUND BRIC B PDFU-2 340 WT

source_name: wildtype_ground_control_solid media plates; BRIC-17; OES chamber: BRIC-B PDFU-2


title: Insulin mutant sample 2

type: SRA

library_source: transcriptomic

organism: Homo sapiens

value: INS C96R heterozygous mutant


title: GROUND BRIC A PDFU-1 331 WT Rep2

source_name: wildtype_ground_control_solid media plates; BRIC-17; OES chamber: BRIC-A PDFU-1


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 adipocyte diff 7d rep1

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description:
H3K27ac_7dAd_BM_rep1
H3K27ac_7dAd_BM.bedGraph.gz
H3K27ac_7dAd_BM.bigWig

library_source: genomic

data_processing:
Quality of all libraries were assessed using FastQC (http://www.bioinformatics.babraham.ac.uk /projects/fastqc/).
ChIP-seq and DNase-seq reads were aligned to the hg19 genome using STAR aligner (Dobin A, et al., Bioinformatics 29:15-21) with the following parameters: --outSJfilterIntronMaxVsReadN 0 --alignIntronMax 1 --alignSJDBoverhangMin 200, with all other parameters set at default. Only one read per position and read length was kept. RNA-seq reads were aligned to hg19 genome using STAR aligner and default settings. Only one read per position and read length was kept.
Regions enriched for open chromatin or MED1 recruitment were identified using the ENCODE IDR (LI Q H, et al. 2011. Annals of Applied Statistics, 5:1752-1779) pipeline and MACS2 peak caller (Zhang Y, et al. 2008. Genome Biology 9:R137). For ChIP-seq samples a pooled Inout control sample was used as control. Reproducible peaks between replicates for the single time points were merged using Homer with distance option -d given.
Gene expression was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -count exons -condenseGenes -noCondensing -noadj. Normalization and differential expression analysis was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) taking Replicates and Time Points into the design matrix, excluding genes which were not detected in both cell lines. Log 2 fold changes and FDR values were calculated with respect to undifferentiated MSC.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph and bigWig files were created using HOMER for visualization of enhancer features in genome browser. Bed files contain reproducible genomic regions from IDR analysis of DNase1-seq, MED1 ChIP-seq and their overlap with and without promoters. Txt file contains non-adjusted gene expression values for eauch replicate and averaged normalized counts and standard errors for each time point as well as FDR and Log2FC with respect to undifferentiated MSC for both BM-hMSC-TERT4 and AT-hMSC-TERT4 cells.

molecule: genomic DNA

source_name: BM-hMSC-TERT4 osteAdlast diff 7d

growth_protocol: Telomerase-immortalized human mesenchymal stromal cells of bone marrow (BM-hMSC-TERT4) or adipose tissue origin (AT-hMSC-TERT) were grown under standard cell culture conditions in α-MEM supplemented with 10 % fetal calf serum (FCS) and 1 % penicillin/streptomycin (P/S).

extract_protocol:
Chromatin was prepared from 150 mm culture dishes first by crosslinking in 1% formaldehyde in PBS (10 minutes, RT). Cross-linking was stopped by adding glycine to a final concentration of 0.125 M (10 minutes, RT). The cells were washed twice in ice-cold PBS, and harvested in ice-cold lysis buffer (0.1% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris pH=8) and sonicated at high setting in a Bioruptor-Twin (Diagenode) at a volume of 1.5 ml in 15-mL tubes for 40 cycles of 30 seconds on and 30 seconds off. The chromatin IPs were performed as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279). Chromatin used for ChIP-seq of MED1 was also cross-linked in 2 mM disuccinimidyl glutarate (DSG) for 20 minutes at RT prior to cross-linking with formaldehyde.
DNase-seq and ChIP-seq libraries were constructed from 10 to 20 ng of genomic DNA according to the manufacturer's instructions (Illumina) as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).

treatment_protocol: Two days post confluency cells were induced to undergo osteoblast or adipocyte differentiation by switched to α-MEM supplemented with 10% FCS, 10 mM dexamethasone, 10 nM vitamin D, 10 mM β-glycerolphosphate, and 50 µg/ml ascorbic acid or to DMEM supplemented with 10% fetal serum, 10ug/mL insulin, 1µM rosiglitazone, 100 mM dexamethasone, and 500 µM isobutylmethylxanthine. Media was replaced on day 2, 4, 7, 9 and 11.

tag: cell line

tag: differentiation status

value: adipocyte

tag: timepoint

tag: chip antibody

value: H3K27ac (ab4729, Abcam)


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 adipocyte diff 3d rep2

description:
H3K27ac_3dAd_BM_rep2
H3K27ac_3dAd_BM.bedGraph.gz
H3K27ac_3dAd_BM.bigWig

source_name: BM-hMSC-TERT4 osteAdlast diff 3d


title: 16HBE_Input

city: Boston

first: Shuibin

last: Lin

address: 1 Blackfan Circle

institute: Boston Childrens Hospital

description: peaks_NSTC2.VS.16HBE\sig_diff_peak NSTC2.VS.16HBE

data_processing:
Library strategy: MeRIP-Seq
Reads were aligned to hg19 using tophat
Peak calling was done with exomePeak
Genome_build: hg19
Supplementary_files_format_and_content: txt file showing the different peak regions and bed file showing significant different peak

molecule: polyA RNA

source_name: bronchi

growth_protocol: RWPE-1 cells were cultured in KSF-M (Fisher Scientific) containing 50 mg/ml bovine pituitary extract, 5 ng/ml epidermal growth factor. SV-HUC-1 cells were cultured in F12K, and 16HBE, NSTC2 cells were cultured in MEM. All medium were supplemented with 10% fetal bovine serum (Gibco, USA), in a humidified air atmosphere of 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from cells using Trizol (Invitrogen) following the manufacturer’s instructions. mRNA was first purified from total RNA using Gen Elute mRNA Miniprep Kit (Sigma-Aldrich). Then 5 ug mRNA was fragmented using a RNA fragmentation kit (Ambion) and immunoprecipitated with the mixture of Protein A beads (Thermo Fisher) and anti-m6A antibody (Synaptic Systems); the immunoprecipitated RNA was washed and eluted by competition with m6A nucleotide solution (Sigma-Aldrich). The purified RNA fragments from m6A MeRIP were used for library construction and sequenced with Illumina Nextseq500.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit.

treatment_protocol: SV-HUC-1 and RWPE-1 cells were maintained continuously in medium containing 10 mM CdCl2 for 8 and 10 weeks, respectively, and then the cells were cultured in cadmium-free medium for 2 weeks.

value: bronchial epithelial

tag: protocol

value: normal

tag: merip antibody


title: 16HBE_m6A

value: m6A (202003 - Synaptic Systems)


title: NSTC2_Input

value: Nickel transformed bronchial epithelial

value: chemical carcinogen transformed


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 adipocyte diff 7d rep2

description:
H3K27ac_7dAd_BM_rep2
H3K27ac_7dAd_BM.bedGraph.gz
H3K27ac_7dAd_BM.bigWig


title: GROUND BRIC A PDFU-1 331 WT Rep1


title: Cd-RWPE-1_m6A

description: peaks_Cd-RWPE-1.VS.RWPE-1\sig_diff_peak Cd-RWPE-1.VS. RWPE-1

source_name: prostate

value: Cd transformed prostate epithelial


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 adipocyte diff 3d rep1

description:
H3K27ac_3dAd_BM_rep1
H3K27ac_3dAd_BM.bedGraph.gz
H3K27ac_3dAd_BM.bigWig


title: Cd-RWPE-1_Input


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 adipocyte diff 1d rep2

description:
H3K27ac_1dAd_BM_rep2
H3K27ac_1dAd_BM.bedGraph.gz
H3K27ac_1dAd_BM.bigWig

source_name: BM-hMSC-TERT4 osteAdlast diff 1d


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 adipocyte diff 14d rep1

description:
H3K27ac_14dAd_BM_rep1
H3K27ac_14dAd_BM.bedGraph.gz
H3K27ac_14dAd_BM.bigWig

source_name: BM-hMSC-TERT4 osteAdlast diff 14d


title: Corrected sample 1

value: Cells of stage 7 pancreatic islet-like aggregates differentiated from iPS cells


title: RWPE-1_m6A

value: prostate epithelial


title: RWPE-1_Input


title: NSTC2_m6A


title: Cd-SV-HUC-1_m6A

description: peaks_Cd-SV-HUC-1.VS.SV-HUC-1\sig_diff_peak Cd-SV-HUC-1.VS. SV-HUC-1

source_name: ureter

value: Cd transformed uroepithelium


title: Cd-SV-HUC-1_Input


title: Insulin mutant sample 1


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 adipocyte diff 1d rep1

description:
H3K27ac_1dAd_BM_rep1
H3K27ac_1dAd_BM.bedGraph.gz
H3K27ac_1dAd_BM.bigWig


title: MC-SV-HUC_T2_m6A

description: peaks_MC-SV-HUC_T2.VS.SV-HUC-1\sig_diff_peak MC-SV-HUC_T2.VS. SV-HUC-1

value: MC transformed uroepithelium


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 adipocyte diff 4h rep2

description:
H3K27ac_4hAd_BM_rep2
H3K27ac_4hAd_BM.bedGraph.gz
H3K27ac_4hAd_BM.bigWig

source_name: BM-hMSC-TERT4 osteAdlast diff 4h


title: FLIGHT BRIC A PDFU-2 302 WT

source_name: wildtype_space_flown_solid media plates; BRIC-17; Dragon,ISS; BRIC-A PDFU-2

value: space flown

value: WT

value: Tissue culture cells

value: RNAlater in-flight fixed_sample


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 adipocyte diff 4h rep1

description:
H3K27ac_4hAd_BM_rep1
H3K27ac_4hAd_BM.bedGraph.gz
H3K27ac_4hAd_BM.bigWig


title: MC-SV-HUC_T2_Input


title: SV-HUC-1_Input

value: uroepithelium


title: SV-HUC-1_m6A


title: FLIGHT BRIC B PDFU-2 304 WT

source_name: wildtype_solid media plates; BRIC-17; Dragon,ISS; BRIC-B PDFU-2space_flown_

value: derived from hypocotyls of WT plant

value: 14 days old


title: FLIGHT BRIC A  PDFU-1 300 WT Rep1

source_name: wildtype_space_flown_solid media plates; BRIC-17; Dragon,ISS; BRIC-A PDFU-1


title: FLIGHT BRIC A PDFU-1 300 WT Rep2


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 undifferentiated rep2

description:
H3K27ac_Msc_BM_rep2
H3K27ac_Msc_BM.bedGraph.gz
H3K27ac_Msc_BM.bigWig

source_name: BM-hMSC-TERT4 undifferentiated

value: undifferentiated

value: H3K27ac (ab4729, Abcam)


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 osteoblast diff 4h rep2

description:
H3K27ac_4hOb_BM_rep2
H3K27ac_4hOb_BM.bedGraph.gz
H3K27ac_4hOb_BM.bigWig

source_name: BM-hMSC-TERT4 osteoblast diff 4h

value: osteoblast


title: CAMTA5 leaf drought overexpression,biological replicate 2

city: lucknow

first: poonam

last: pant

state: utter pradesh

address: Rana Pratap Marg

department: plant molecular biology

country: India

institute: NBRI

description: SAMPLE 14

hyb_protocol: According to affymatrix gene chip instruction manual using Fluidisc station 450.

scan_protocol: GeneChips were scanned using Affymatrix gene chip scanner.

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.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.2.1.20

source_name: CAMTA5 leaf drought overexpression

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: 1 month old Arabidopsis plant

extract_protocol: Total RNA isolated from plant total RNA sigma kit

treatment_protocol: Plant sample collected under water and 14 days drought condition

tag: ecotype background

tag: genotype/variation

value: CAMTA5 Overexpresion (OX-5)

value: 1 month-old plant

tag: collected under

value: 14 days drought condition

tag: tissue

value: leaf


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 undifferentiated rep1

description:
H3K27ac_Msc_BM_rep1
H3K27ac_Msc_BM.bedGraph.gz
H3K27ac_Msc_BM.bigWig


title: FLIGHT BRIC B PDFU-1 303 WT

source_name: wildtype_solid media plates; BRIC-17; Dragon,ISS; BRIC-B PDFU-1space_flown_

tag: flight status


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 osteoblast diff 1d rep2

description:
H3K27ac_1dOb_BM_rep2
H3K27ac_1dOb_BM.bedGraph.gz
H3K27ac_1dOb_BM.bigWig

source_name: BM-hMSC-TERT4 osteoblast diff 1d


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 osteoblast diff 3d rep2

description:
H3K27ac_3dOb_BM_rep2
H3K27ac_3dOb_BM.bedGraph.gz
H3K27ac_3dOb_BM.bigWig

source_name: BM-hMSC-TERT4 osteoblast diff 3d


title: camta5 leaf drought,biological replicate 2

description: SAMPLE 11

source_name: camta5 leaf drought

value: camta5-a mutant


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 osteoblast diff 3d rep1

description:
H3K27ac_3dOb_BM_rep1
H3K27ac_3dOb_BM.bedGraph.gz
H3K27ac_3dOb_BM.bigWig


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 osteoblast diff 7d rep2

description:
H3K27ac_7dOb_BM_rep2
H3K27ac_7dOb_BM.bedGraph.gz
H3K27ac_7dOb_BM.bigWig

source_name: BM-hMSC-TERT4 osteoblast diff 7d


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 osteoblast diff 7d rep1

description:
H3K27ac_7dOb_BM_rep1
H3K27ac_7dOb_BM.bedGraph.gz
H3K27ac_7dOb_BM.bigWig


title: MED1 ChIP-seq, BM-hMSC-TERT4 adipocyte diff 14d rep2

description:
MED1_14dAd_BM_rep2
MED1_14dAd_BM.bedGraph.gz
MED1_14dAd_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed

value: adipocyte

value: MED1 (M-255, sc-8998, Santa Cruz)


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 osteoblast diff 1d rep1

description:
H3K27ac_1dOb_BM_rep1
H3K27ac_1dOb_BM.bedGraph.gz
H3K27ac_1dOb_BM.bigWig


title: CAMTA5 leaf drought overexpression,biological replicate 1

description: SAMPLE 13


title: PSP, histologically confirmed diagnose, case 292

type: genomic

city: Evry

first: Jorg

last: Tost

address: 2 rue Gaston Cremieux

country: France

institute: CEA-Institut de Genomique, Centre National de Genotypage

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium Human Methylation 450 K bead arrays (Illumina Inc., San Diego, CA). Processing was done according to the manufacturer’s protocol using an automated pipeline.  of bisulfite-treated DNA was analyzed using the Infinium  Human Methylation 450 K bead arrays spanning approximately  over 480,000 CpG sites/sample (Illumina Inc., San  Diego, CA). Processing was done according to the manufacturer’s  protocol using an automated pipeline, and the  arrays were scanned on an Illumina iScan platform (Illumina  Inc., San Diego, CA) established at the Life & Brain  Center (Bonn, Germany)

data_processing:
Subset quantile normalization, revised version of Touleimat & tost, Epigenomics 2012
The normalized.txt contains normalized Beta values.

label: Cy5 and Cy3

source_name: PSP_frontal cortex, post mortem tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from post-mortem brain samples using Qiagen DNeasy Kit according to standard instructions

tag: subject group

value: progressive supranuclear palsy (PSP)

tag: subject status

value: histologically confirmed diagnose

tag: subject id

value: case 292

tag: gender

value: male

tag: age at death

tag: tssue

value: frontal cortex, post mortem tissue

tag: molecule subtype

value: bisulfite converted DNA from brain tissue


title: PSP, histologically confirmed diagnose, case 290

scan_protocol: the arrays were scanned on an Illumina iScan platform

value: case 290


title: PSP, histologically confirmed diagnose, case 289

value: case 289

value: female


title: PSP, histologically confirmed diagnose, case 291

value: case 291


title: PSP, histologically confirmed diagnose, case 293

value: case 293


title: MED1 ChIP-seq, BM-hMSC-TERT4 adipocyte diff 14d rep1

description:
MED1_14dAd_BM_rep1
MED1_14dAd_BM.bedGraph.gz
MED1_14dAd_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed

tag: cell line

tag: differentiation status


title: MED1 ChIP-seq, BM-hMSC-TERT4 adipocyte diff 7d rep2

description:
MED1_7dAd_BM_rep2
MED1_7dAd_BM.bedGraph.gz
MED1_7dAd_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed

source_name: BM-hMSC-TERT4 osteAdlast diff 7d

tag: timepoint

tag: chip antibody


title: MED1 ChIP-seq, BM-hMSC-TERT4 adipocyte diff 3d rep2

description:
MED1_3dAd_BM_rep2
MED1_3dAd_BM.bedGraph.gz
MED1_3dAd_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed

source_name: BM-hMSC-TERT4 osteAdlast diff 3d


title: MED1 ChIP-seq, BM-hMSC-TERT4 adipocyte diff 7d rep1

description:
MED1_7dAd_BM_rep1
MED1_7dAd_BM.bedGraph.gz
MED1_7dAd_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed


title: camta5 leaf water,biological replicate 1

description: SAMPLE 7

source_name: camta5 leaf water

value: wild type

tag: age

value: 1 month-old plant

value: water condition


title: PSP, histologically confirmed diagnose, case 294

value: case 294


title: camta5 leaf drought,biological replicate 1

description: SAMPLE 10

tag: ecotype background

value: camta5-a mutant

value: 14 days drought condition

value: leaf


title: camta5 leaf water,biological replicate 2

description: SAMPLE 8

tag: genotype/variation


title: Col-0 leaf drought, biological replicate 2

description: SAMPLE 5

source_name: Col-0 leaf drought

tag: collected under


title: camta5 leaf water,biological replicate 3

description: SAMPLE 9

tag: tissue


title: camta5 leaf drought,biological replicate 3

description: SAMPLE 12


title: Col-0 leaf drought, biological replicate 3

description: SAMPLE 6


title: Col-0 leaf water, biological replicate 3

description: SAMPLE 3

source_name: Col-0 leaf water


title: Col-0 leaf water, biological replicate 2

description: SAMPLE 2


title: MED1 ChIP-seq, BM-hMSC-TERT4 adipocyte diff 3d rep1

description:
MED1_3dAd_BM_rep1
MED1_3dAd_BM.bedGraph.gz
MED1_3dAd_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed

value: adipocyte

value: MED1 (M-255, sc-8998, Santa Cruz)


title: Col-0 leaf drought, biological replicate 1

description: SAMPLE 4


title: MED1 ChIP-seq, BM-hMSC-TERT4 adipocyte diff 1d rep1

description:
MED1_1dAd_BM_rep1
MED1_1dAd_BM.bedGraph.gz
MED1_1dAd_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed

source_name: BM-hMSC-TERT4 osteAdlast diff 1d


title: PSP, histologically confirmed diagnose, case 288

value: progressive supranuclear palsy (PSP)

value: histologically confirmed diagnose

value: case 288


title: PSP, histologically confirmed diagnose, case 285

value: case 285

value: male

value: frontal cortex, post mortem tissue

value: bisulfite converted DNA from brain tissue


title: Col-0 leaf water, biological replicate 1

description: SAMPLE 1


title: MED1 ChIP-seq, BM-hMSC-TERT4 adipocyte diff 4h rep2

description:
MED1_4hAd_BM_rep2
MED1_4hAd_BM.bedGraph.gz
MED1_4hAd_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed

source_name: BM-hMSC-TERT4 osteAdlast diff 4h


title: PSP, histologically confirmed diagnose, case 284

value: case 284


title: MED1 ChIP-seq, BM-hMSC-TERT4 adipocyte diff 4h rep1

description:
MED1_4hAd_BM_rep1
MED1_4hAd_BM.bedGraph.gz
MED1_4hAd_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed


title: PSP, histologically confirmed diagnose, case 283

value: case 283


title: MED1 ChIP-seq, BM-hMSC-TERT4 undifferentiated rep1

description:
MED1_Msc_BM_rep1
MED1_Msc_BM.bedGraph.gz
MED1_Msc_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed

value: undifferentiated


title: MED1 ChIP-seq, BM-hMSC-TERT4 undifferentiated rep2

description:
MED1_Msc_BM_rep2
MED1_Msc_BM.bedGraph.gz
MED1_Msc_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed


title: PSP, histologically confirmed diagnose, case 279

value: case 279


title: PSP, histologically confirmed diagnose, case 280

value: case 280


title: MED1 ChIP-seq, BM-hMSC-TERT4 osteoblast diff 4h rep2

description:
MED1_4hOb_BM_rep2
MED1_4hOb_BM.bedGraph.gz
MED1_4hOb_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed

value: osteoblast


title: MED1 ChIP-seq, BM-hMSC-TERT4 adipocyte diff 1d rep2

description:
MED1_1dAd_BM_rep2
MED1_1dAd_BM.bedGraph.gz
MED1_1dAd_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed


title: PSP, histologically confirmed diagnose, case 286

value: case 286


title: MED1 ChIP-seq, BM-hMSC-TERT4 osteoblast diff 1d rep2

description:
MED1_1dOb_BM_rep2
MED1_1dOb_BM.bedGraph.gz
MED1_1dOb_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed


title: MED1 ChIP-seq, BM-hMSC-TERT4 osteoblast diff 4h rep1

description:
MED1_4hOb_BM_rep1
MED1_4hOb_BM.bedGraph.gz
MED1_4hOb_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed


title: PSP, histologically confirmed diagnose, case 275

value: case 275

value: female


title: MED1 ChIP-seq, BM-hMSC-TERT4 osteoblast diff 1d rep1

description:
MED1_1dOb_BM_rep1
MED1_1dOb_BM.bedGraph.gz
MED1_1dOb_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed

value: MED1 (M-255, sc-8998, Santa Cruz)


title: PSP, histologically confirmed diagnose, case 277

value: progressive supranuclear palsy (PSP)

value: case 277


title: MED1 ChIP-seq, BM-hMSC-TERT4 osteoblast diff 3d rep1

description:
MED1_3dOb_BM_rep1
MED1_3dOb_BM.bedGraph.gz
MED1_3dOb_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed


title: PSP, histologically confirmed diagnose, case 274

value: histologically confirmed diagnose

value: case 274


title: PSP, histologically confirmed diagnose, case 281

value: case 281


title: PSP, histologically confirmed diagnose, case 276

value: case 276

value: male

value: frontal cortex, post mortem tissue


title: MED1 ChIP-seq, BM-hMSC-TERT4 osteoblast diff 7d rep2

description:
MED1_7dOb_BM_rep2
MED1_7dOb_BM.bedGraph.gz
MED1_7dOb_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed


title: PSP, histologically confirmed diagnose, case 282

value: case 282

value: bisulfite converted DNA from brain tissue


title: DNase-seq, BM-hMSC-TERT4 adipocyte diff 14d rep2

description:
DNase1_14dAd_BM_rep2
DNase1_14dAd_BM.bedGraph
DNase1_14dAd_BM.bigWig
DNase1_IDR_peaks.bed

source_name: BM-hMSC-TERT4 osteAdlast diff 14d

extract_protocol:
Nuclei were isolated from cells grown on 150 mm dishes using a 0.04% NP-40 buffer (15 mM Tris-HCl pH=8.0, 15 mM NaCl, 60 mM KCl, 1 mM EDTA pH=8.0, 0.5 mM EGTA pH=8.0, 0.5 mM Spermidine). 10 million freshly isolated nuclei were treated with 40 units/ml DNase I for 3 minutes at 37°C as decribed previously (Siersbaek R, et al.2011. EMBO Journal 30:1459-72). After RNase and Proteinase K treatment, DNA was isolated by phenol-chloroform-extraction and separated by ultra-centrifugation on a sucrose gradient overnight. DNA-fragments between 100 and 500 bp (representing 2-hit cutting events) were isolated, checked for enrichment of open chromatin over background using real- time PCR.
DNase-seq and ChIP-seq libraries were constructed from 10 to 20 ng of genomic DNA according to the manufacturer's instructions (Illumina) as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).

value: adipocyte


title: PSP, histologically confirmed diagnose, case 272

value: case 272


title: PSP, histologically confirmed diagnose, case 278

value: case 278


title: PSP, histologically confirmed diagnose, case 269

value: case 269


title: PSP, histologically confirmed diagnose, case 270

value: case 270


title: DNase-seq, BM-hMSC-TERT4 adipocyte diff 7d rep2

description:
DNase1_7dAd_BM_rep2
DNase1_7dAd_BM.bedGraph
DNase1_7dAd_BM.bigWig
DNase1_IDR_peaks.bed


title: DNase-seq, BM-hMSC-TERT4 adipocyte diff 14d rep1

description:
DNase1_14dAd_BM_rep1
DNase1_14dAd_BM.bedGraph
DNase1_14dAd_BM.bigWig
DNase1_IDR_peaks.bed


title: DNase-seq, BM-hMSC-TERT4 adipocyte diff 7d rep1

description:
DNase1_7dAd_BM_rep1
DNase1_7dAd_BM.bedGraph
DNase1_7dAd_BM.bigWig
DNase1_IDR_peaks.bed


title: MED1 ChIP-seq, BM-hMSC-TERT4 osteoblast diff 7d rep1

description:
MED1_7dOb_BM_rep1
MED1_7dOb_BM.bedGraph.gz
MED1_7dOb_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed

value: osteoblast


title: PSP, histologically confirmed diagnose, case 268

value: case 268


title: PSP, histologically confirmed diagnose, case 271

value: progressive supranuclear palsy (PSP)

value: case 271


title: PSP, histologically confirmed diagnose, case 267

value: histologically confirmed diagnose

value: case 267

value: female


title: PSP, histologically confirmed diagnose, case 266

value: case 266


title: DNase-seq, BM-hMSC-TERT4 adipocyte diff 3d rep2

description:
DNase1_3dAd_BM_rep2
DNase1_3dAd_BM.bedGraph
DNase1_3dAd_BM.bigWig
DNase1_IDR_peaks.bed


title: PSP, histologically confirmed diagnose, case 273

value: case 273


title: H3K27ac ChIP-seq, BM-hMSC-TERT4 osteoblast diff 4h rep1

description:
H3K27ac_4hOb_BM_rep1
H3K27ac_4hOb_BM.bedGraph.gz
H3K27ac_4hOb_BM.bigWig

value: H3K27ac (ab4729, Abcam)


title: PSP, histologically confirmed diagnose, case 265

value: case 265

value: frontal cortex, post mortem tissue


title: MED1 ChIP-seq, BM-hMSC-TERT4 osteoblast diff 3d rep2

description:
MED1_3dOb_BM_rep2
MED1_3dOb_BM.bedGraph.gz
MED1_3dOb_BM.bigWig
MED1_IDR_peaks.bed
MED1_IDR_in_DNase1_peaks.bed
MED1_IDR_in_DNase1_peaks_nonPromoter.bed

value: MED1 (M-255, sc-8998, Santa Cruz)


title: 550536A12 - CUC_B_rep2 vs Col_B_rep2

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Identification of genes specifically targeted by the CUC2 transcription factor that defines the margins of the floral meristem of Arabidopsis thaliana.

hyb_protocol: Col_B_rep2 Cy5 / CUC_B_rep2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, total RNA  .

growth_protocol: flower bud - Media: Soil composed of blonde peat (70%), brown peat (30%) and clay ( 60kg/m3). Period 1: 4-5 weeks; Period 2: 5-6 weeks. Hygrometry: period 1:65-75% / period 2:50-65% Temperature: period 1:19°C (day), 16°C (night) period 2:21°C (day), 17°C (night) Light: period 1:Plants were grown under short-day conditions (8 h light/16 h darkness) for 4 to 5 weeks to synchronize them. perido 2:4 to 5 weeks after seeding, plants were transferred in long-day conditions (12 h light/12 h darkness).

extract_protocol: Col_B_rep2:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: Columbia

tag: genotype

value: control

tag: developmental stage

value: (Boyes et al. Plant Cell 2001):boyes:6.10

extract_protocol: CUC_B_rep2:10ug. (Qiagen_RNeasy.pdf)

value: CUC mutant


title: DNase-seq, BM-hMSC-TERT4 adipocyte diff 1d rep2

description:
DNase1_1dAd_BM_rep2
DNase1_1dAd_BM.bedGraph
DNase1_1dAd_BM.bigWig
DNase1_IDR_peaks.bed

value: adipocyte


title: DNase-seq, BM-hMSC-TERT4 adipocyte diff 4h rep2

description:
DNase1_4hAd_BM_rep2
DNase1_4hAd_BM.bedGraph
DNase1_4hAd_BM.bigWig
DNase1_IDR_peaks.bed


title: 550536A11 - Col_B_rep2 vs CUC_B_rep2

hyb_protocol: CUC_B_rep2 Cy5 / Col_B_rep2 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: 550540A01 - Col_C_rep3 vs CUC_C_rep3

hyb_protocol: CUC_C_rep3 Cy5 / Col_C_rep3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

extract_protocol: CUC_C_rep3:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: Col_C_rep3:10ug. (Qiagen_RNeasy.pdf)


title: 550536A10 - CUC_A_rep1 vs Col_A_rep1

hyb_protocol: Col_A_rep1 Cy5 / CUC_A_rep1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

extract_protocol: Col_A_rep1:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: CUC_A_rep1:10ug. (Qiagen_RNeasy.pdf)


title: 550536A09 - Col_A_rep1 vs CUC_A_rep1

hyb_protocol: CUC_A_rep1 Cy5 / Col_A_rep1 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)


title: DNase-seq, BM-hMSC-TERT4 adipocyte diff 4h rep1

description:
DNase1_4hAd_BM_rep1
DNase1_4hAd_BM.bedGraph
DNase1_4hAd_BM.bigWig
DNase1_IDR_peaks.bed


title: DNase-seq, BM-hMSC-TERT4 adipocyte diff 3d rep1

description:
DNase1_3dAd_BM_rep1
DNase1_3dAd_BM.bedGraph
DNase1_3dAd_BM.bigWig
DNase1_IDR_peaks.bed


title: PSP, histologically confirmed diagnose, case 263

tag: subject group

tag: subject status

tag: subject id

value: case 263

value: bisulfite converted DNA from brain tissue


title: DNase-seq, BM-hMSC-TERT4 undifferentiated rep2

description:
DNase1_Msc_BM_rep2
DNase1_Msc_BM.bedGraph
DNase1_Msc_BM.bigWig
DNase1_IDR_peaks.bed

source_name: BM-hMSC-TERT4 undifferentiated

value: undifferentiated


title: Tie2 Control 1

city: Cincinnati

first: Andrew

last: Potter

state: OH

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

description:
Gene expression of FACS-purified control endothelial cells
Tie2_NRPKM_2_15_17.xlsx
Tie2_CTRL_66

data_processing:
Samples were aligned to the mm9 genome using TopHat v1.4.1. Known junctions from the RefSeq database were provided to TopHat with the -G option.
Prior to quantitation, reads were filtered on genic region, retaining reads mapping to spliced, partial genic, exonic, exon/intron junction, and genic. Reads were also filtered according to quality metrics: Retained reads with quality threshold >= 20, N's allowed in read <= 0, number of multiple matches allowed <= 1, reads failing vendor QC were also removed. Also filtered on duplicate reads, with duplicate threshold of 4.
The generation of NRPKM data was carried out using Strand NGS 2.6 (Strand). Read density (NRPKM) in Strand NGS is computed as the normalized read count (DESeq) per kilo base of exon model per million reads. This is similar to the standard RPKM used in the literature except that it is computed on the normalized read count rather than on the raw read count.
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadsheet including NRPKM values for each sample in Series.

organism: Mus musculus

source_name: kidney glomerular cells

extract_protocol:
RNA was purified using the Zymo ZR RNA MicroPrep kit (cat. No R1061). Nugen Ovation RNA-Seq V2 was used for amplification.
The initial amplification step for all  samples was done with the NuGEN Ovation RNA-Seq System v2. The assay was used to amplify RNA samples to create double stranded cDNA. The concentrations were measured using the Qubit dsDNA BR assay. Libraries were then created for all samples. Specifically, the Illumina protocol, the Nextera XT DNA Sample Preparation Kit, was used to create DNA library templates from the double stranded cDNA. The concentrations were measured using the Qubit dsDNA HS assay. The size of the libraries for each sample was measured using the Agilent HS DNA chip. The samples were placed in a pool. The concentration of the pool is optimized to acquire at least  15-20 million reads per sample.

treatment_protocol: 3-allele (Mutant) mice have urinary albumin excretion > 30 mg/dL as quantified by SDS-page gel electrophoresis prior to harvest; control (wild-type or 1 Fyn allele deleted) mice have no detectable urinary albumin excretion via prior to harvest. Kidney phenotype is confirmed by blood collection at time of harvest analysis measuring serum BUN, albumin, creatinine and cholesterol), histology and EM.

tag: cell type

value: Endothelial

tag: age at harvest

value: 15 months


title: DNase-seq, BM-hMSC-TERT4 adipocyte diff 1d rep1

description:
DNase1_1dAd_BM_rep1
DNase1_1dAd_BM.bedGraph
DNase1_1dAd_BM.bigWig
DNase1_IDR_peaks.bed

tag: cell line


title: DNase-seq, BM-hMSC-TERT4 osteoblast diff 4h rep2

description:
DNase1_4hOb_BM_rep2
DNase1_4hOb_BM.bedGraph
DNase1_4hOb_BM.bigWig
DNase1_IDR_peaks.bed

source_name: BM-hMSC-TERT4 osteoblast diff 4h

tag: differentiation status

value: osteoblast


title: Tie2 Control 3

description:
Gene expression of FACS-purified control endothelial cells
Tie2_NRPKM_2_15_17.xlsx
Tie2_CTRL_103

value: 14 months


title: PSP, histologically confirmed diagnose, case 261

value: progressive supranuclear palsy (PSP)

value: histologically confirmed diagnose

value: case 261

tag: gender

value: male

tag: age at death

tag: tssue

tag: molecule subtype


title: PSP, histologically confirmed diagnose, case 260

value: case 260

value: female

value: frontal cortex, post mortem tissue


title: DNase-seq, BM-hMSC-TERT4 undifferentiated rep1

description:
DNase1_Msc_BM_rep1
DNase1_Msc_BM.bedGraph
DNase1_Msc_BM.bigWig
DNase1_IDR_peaks.bed

tag: timepoint

tag: chip antibody


title: Meis Control 3

description:
Gene expression of FACS-purified control mesangial cells
Meis_NRPKM_2_15_17.xlsx
Meis_CTRL_142

value: Mesangial

value: 11 months


title: Tie2 Mutant 2

description:
Gene expression of FACS-purified mutant endothelial cells
Tie2_NRPKM_2_15_17.xlsx
Tie2_3A_114

value: 7.5 months


title: Meis Control 1

description:
Gene expression of FACS-purified control mesangial cells
Meis_NRPKM_2_15_17.xlsx
Meis_CTRL_54

value: 5 months


title: Tie2 Mutant 3

description:
Gene expression of FACS-purified mutant endothelial cells
Tie2_NRPKM_2_15_17.xlsx
131_Tie2_3A

value: 18 months


title: Meis Mutant 3

description:
Gene expression of FACS-purified mutant mesangial cells
Meis_NRPKM_2_15_17.xlsx
Meis_3A_122

value: 12 months


title: Tie2 Control 2

description:
Gene expression of FACS-purified control endothelial cells
Tie2_NRPKM_2_15_17.xlsx
Tie2_CTRL_101

value: Endothelial

value: 12.5 months


title: Meis Control 2

description:
Gene expression of FACS-purified control mesangial cells
Meis_NRPKM_2_15_17.xlsx
Meis_CTRL_84


title: Meis Mutant 2

description:
Gene expression of FACS-purified mutant mesangial cells
Meis_NRPKM_2_15_17.xlsx
Meis_3A_80

value: 15 months


title: DNase-seq, BM-hMSC-TERT4 osteoblast diff 1d rep2

description:
DNase1_1dOb_BM_rep2
DNase1_1dOb_BM.bedGraph
DNase1_1dOb_BM.bigWig
DNase1_IDR_peaks.bed

value: osteoblast


title: Meis Mutant 1

description:
Gene expression of FACS-purified mutant mesangial cells
Meis_NRPKM_2_15_17.xlsx
Meis_3A_43


title: PSP, histologically confirmed diagnose, case 258

value: progressive supranuclear palsy (PSP)

value: case 258

value: bisulfite converted DNA from brain tissue


title: DNase-seq, BM-hMSC-TERT4 osteoblast diff 1d rep1

description:
DNase1_1dOb_BM_rep1
DNase1_1dOb_BM.bedGraph
DNase1_1dOb_BM.bigWig
DNase1_IDR_peaks.bed


title: MAFB Control 3

description:
Gene expression of FACS-purified control MAFB podocytes
MAFB_NRPKM_2_15_17.xlsx
350_MAFB_CTRL

extract_protocol:
RNA was purified using the Norgen Single Cell RNA Purification Kit (cat. Num. 51800). Nugen Ovation RNA-Seq V2 was used for amplification.
The initial amplification step for all  samples was done with the NuGEN Ovation RNA-Seq System v2. The assay was used to amplify RNA samples to create double stranded cDNA. The concentrations were measured using the Qubit dsDNA BR assay. Libraries were then created for all samples. Specifically, the Illumina protocol, the Nextera XT DNA Sample Preparation Kit, was used to create DNA library templates from the double stranded cDNA. The concentrations were measured using the Qubit dsDNA HS assay. The size of the libraries for each sample was measured using the Agilent HS DNA chip. The samples were placed in a pool. The concentration of the pool is optimized to acquire at least  15-20 million reads per sample.

value: Podocytes


title: PSP, histologically confirmed diagnose, case 264

value: histologically confirmed diagnose

value: case 264


title: PSP, histologically confirmed diagnose, case 257

value: case 257

value: female

value: frontal cortex, post mortem tissue


title: MAFB Control 2

description:
Gene expression of FACS-purified control MAFB podocytes
MAFB_NRPKM_2_15_17.xlsx
285_MAFB_CTRL


title: MAFB Mutant 2

description:
Gene expression of FACS-purified mutant MAFB podocytes
MAFB_NRPKM_2_15_17.xlsx
300_MAFB_3A

value: 13 months


title: MAFB Control 1

description:
Gene expression of FACS-purified control MAFB podocytes
MAFB_NRPKM_2_15_17.xlsx
538_MAFB_CTRL

value: 7.5 months


title: MAFB Mutant 3

description:
Gene expression of FACS-purified mutant MAFB podocytes
MAFB_NRPKM_2_15_17.xlsx
342_MAFB_3A


title: MAFB Mutant 1

description:
Gene expression of FACS-purified mutant MAFB podocytes
MAFB_NRPKM_2_15_17.xlsx
468_9_MAFB_3A

value: 9 months


title: DNase-seq, BM-hMSC-TERT4 osteoblast diff 3d rep1

description:
DNase1_3dOb_BM_rep1
DNase1_3dOb_BM.bedGraph
DNase1_3dOb_BM.bigWig
DNase1_IDR_peaks.bed


title: NK Combo 3

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (29), aligned to the human genome using STAR (30), and quantified transcript counts using HTSeq (31). Raw read counts were normalized to FPKM value for analysis.
Genome_build: Reads were aligned to the transcriptome (hg19, GRCh37.75)
Supplementary_files_format_and_content: Tab-delimited text file includes normalized FPKM value for each sample

source_name: NK cells from lung tumors

growth_protocol: For in vitro studies, cells were maintained in DMEM or RPMI supplemented with 10%  FBS and 100 IU/ml penicillin/streptomycin. For in vivo studies, female C57BL/6 mice were transplanted with KP lung tumor cells by tail vein injection. Treatment began one week post-transplantation following confirmation of lung tumor engraftment by bioluminescent imaging.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate  condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: For in vitro studies, cells were treated for 8 days with vehicle (DMSO), trametinib (25 nM), palbociclib (500nM), or both in combination. Drug media was changed every 3 days. For in vivo studies, mice were treated for 1 week with vehicle or combined trametinib (1 mg/kg body weight) or palbociclib (100 mg/kg body weight).

value: CD45+CD3-NK1.1+ NK cell

tag: treatment

value: Combination


title: DNase-seq, BM-hMSC-TERT4 osteoblast diff 4h rep1

description:
DNase1_4hOb_BM_rep1
DNase1_4hOb_BM.bedGraph
DNase1_4hOb_BM.bigWig
DNase1_IDR_peaks.bed


title: NK Combo 4


title: DNase-seq, BM-hMSC-TERT4 osteoblast diff 7d rep2

description:
DNase1_7dOb_BM_rep2
DNase1_7dOb_BM.bedGraph
DNase1_7dOb_BM.bigWig
DNase1_IDR_peaks.bed


title: PSP, histologically confirmed diagnose, case 255

value: case 255

value: male


title: DNase-seq, BM-hMSC-TERT4 osteoblast diff 3d rep2

description:
DNase1_3dOb_BM_rep2
DNase1_3dOb_BM.bedGraph
DNase1_3dOb_BM.bigWig
DNase1_IDR_peaks.bed

value: osteoblast


title: PSP, histologically confirmed diagnose, case 259

value: progressive supranuclear palsy (PSP)

value: case 259


title: PSP, histologically confirmed diagnose, case 256

value: case 256

value: bisulfite converted DNA from brain tissue


title: 550540A02 - CUC_C_rep3 vs Col_C_rep3

description: Identification of genes specifically targeted by the CUC2 transcription factor that defines the margins of the floral meristem of Arabidopsis thaliana.

hyb_protocol: Col_C_rep3 Cy5 / CUC_C_rep3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)

tag: ecotype

value: Columbia

value: control

tag: age

value: (Boyes et al. Plant Cell 2001):boyes:6.10

value: CUC mutant


title: DNase-seq, BM-hMSC-TERT4 osteoblast diff 7d rep1

description:
DNase1_7dOb_BM_rep1
DNase1_7dOb_BM.bedGraph
DNase1_7dOb_BM.bigWig
DNase1_IDR_peaks.bed


title: PSP, histologically confirmed diagnose, case 254

value: histologically confirmed diagnose

value: case 254

value: frontal cortex, post mortem tissue


title: NK Combo 2


title: PSP, histologically confirmed diagnose, case 252

value: case 252


title: NK Vehicle 4

value: CD45+CD3-NK1.1+ NK cell

value: Vehicle


title: NK Vehicle 5


title: NK Vehicle 2


title: NK Vehicle 3


title: NK Vehicle 1


title: PSP, histologically confirmed diagnose, case 251

value: case 251


title: PSP, histologically confirmed diagnose, case 250

value: case 250

value: female


title: S--T15

city: Clermont-Ferrand

first: David

middle: H

last: VOLLE

address: 28 place Henri Dunant

institute: INSERM

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and CASAVA 1.8.2.
Sequenced reads were trimmed for adaptor sequence, the number of reads corresponds to reads without adapter dimer. The average base quality of 95% of the positions of the reads must be over 30 to pass the platform criteria. A base quality of 30 means that there 1 chance out of 1000 that a given base has been miscalled during the Base Calling (i.e. probability of error = 0.001)
Version 0.11.2 was run using the following arguments --nogroup --casava. Version 0.5.1 was run using the following arguments: --subset 1000000 --bowtie '-p 2'. The --subset option asks FastQScreen to use only a subset of reads to be mapped on genomes/DNA sequences.
Reads were mapped onto the mm10 assembly of the mouse genome using Tophat v2.0.10 (Kim et al., 2013) and the bowtie2 v2.1.0 aligner (Langmead et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Testis

extract_protocol:
Testis were removed, flash frozen on dry ice, and RNA was harvested using Nucleospin RNA L (Macherey-Nagel, Hoerdt, France). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: testis

tag: age/genotype

value: potsnatal day 10; FXR KO

value: Stigmasterol


title: PSP, histologically confirmed diagnose, case 249

tag: subject group

value: progressive supranuclear palsy (PSP)

tag: subject status

tag: subject id

value: case 249

value: male

value: bisulfite converted DNA from brain tissue


title: S--T10


title: PSP, histologically confirmed diagnose, case 248

value: case 248


title: BPA--T117

value: bisphenol-A


title: NK Combo 1

value: Combination


title: BPA--T83


title: S--T93


title: BPA--T25


title: veh--T110


title: Tie2 Mutant 1

description:
Gene expression of FACS-purified mutant endothelial cells
Tie2_NRPKM_2_15_17.xlsx
Tie2_3A_43

tag: cell type

value: Endothelial

tag: age at harvest

value: 14.5 months

tag: genotype


title: veh--T90


title: PSP, histologically confirmed diagnose, case 247

value: histologically confirmed diagnose

value: case 247

tag: gender

tag: age at death

value: frontal cortex, post mortem tissue


title: PSP, histologically confirmed diagnose, case 262

value: case 262

tag: tssue

tag: molecule subtype


title: PSP, histologically confirmed diagnose, case 246

value: case 246


title: PSP, histologically confirmed diagnose, case 253

value: case 253


title: veh--T1

value: testis

value: potsnatal day 10; FXR KO

value: Vehicle


title: S++T119

value: potsnatal day 10; wild-type

value: Stigmasterol


title: PSP, histologically confirmed diagnose, case 243

value: progressive supranuclear palsy (PSP)

value: case 243

value: female

value: bisulfite converted DNA from brain tissue


title: PSP, histologically confirmed diagnose, case 245

value: case 245

value: male


title: S++T78


title: BPA++T61

value: bisphenol-A


title: S++T98


title: BPA++T74


title: BPA++T75


title: PSP, histologically confirmed diagnose, case 242

value: histologically confirmed diagnose

value: case 242


title: BPA++T60


title: PSP, histologically confirmed diagnose, case 241

value: case 241

value: frontal cortex, post mortem tissue


title: S++T118


title: PSP, histologically confirmed diagnose, case 244

value: case 244


title: veh++T66

value: testis


title: veh++T79


title: veh++T81


title: PSP, histologically confirmed diagnose, case 240

value: case 240


title: veh++T71

value: Vehicle


title: PSP, histologically confirmed diagnose, case 239

value: case 239


title: PSP, histologically confirmed diagnose, case 238

value: case 238


title: PSP, histologically confirmed diagnose, case 237

value: progressive supranuclear palsy (PSP)

value: case 237


title: PSP, histologically confirmed diagnose, case 236

value: case 236


title: PSP, histologically confirmed diagnose, case 235

value: case 235

value: female

value: bisulfite converted DNA from brain tissue


title: PSP, histologically confirmed diagnose, case 234

value: case 234


title: PSP, histologically confirmed diagnose, case 233

value: histologically confirmed diagnose

value: case 233

value: male


title: PSP, histologically confirmed diagnose, case 232

value: case 232

value: frontal cortex, post mortem tissue


title: PSP, histologically confirmed diagnose, case 231

value: case 231


title: PSP, histologically confirmed diagnose, case 229

value: case 229


title: PSP, histologically confirmed diagnose, case 230

value: case 230


title: PSP, histologically confirmed diagnose, case 227

value: case 227


title: PSP, histologically confirmed diagnose, case 226

value: case 226


title: PSP, histologically confirmed diagnose, case 225

value: progressive supranuclear palsy (PSP)

value: case 225


title: Case4_5

city: Manchester

first: Richard

last: Marais

address: Wilmslow Road

department: Molecular Oncology

country: United Kingdom

institute: Cancer Research UK Manchester Institute

description: tumour prostate sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: minfi R

source_name: Prostectomy 9_tumour prostate sample

extract_protocol: DNA was extracted and purified from fresh/frozen prostate tissue samples using Qiagen DNA/RNA Kit according to standard instructions

value: Male

tag: sample type

value: Prostectomy 9

tag: disease state

value: Tumour


title: Case2_3

description: tumour prostate sample

source_name: Prostectomy 7_tumour prostate sample

value: Prostectomy 7


title: Case2_5

description: tumour prostate sample


title: Case4_8

description: tumour prostate sample


title: Case4_2

description: tumour prostate sample


title: Case2_4

description: tumour prostate sample


title: Case4_7

description: normal prostate sample

source_name: Prostectomy 9_normal prostate sample

value: Normal


title: PSP, histologically confirmed diagnose, case 228

source_name: PSP_frontal cortex, post mortem tissue

value: histologically confirmed diagnose

value: case 228

value: female

value: bisulfite converted DNA from brain tissue


title: Case2_2

description: tumour prostate sample


title: Case2_7

description: normal prostate sample

source_name: Prostectomy 7_normal prostate sample


title: PSP, histologically confirmed diagnose, case 223

value: case 223

value: frontal cortex, post mortem tissue


title: Case6_6

description: normal prostate sample

source_name: Prostectomy 5_normal prostate sample

value: Prostectomy 5


title: PSP, histologically confirmed diagnose, case 222

value: case 222


title: Case4_6

description: tumour prostate sample


title: PSP, histologically confirmed diagnose, case 224

value: case 224

value: male


title: Case1_6

description: tumour prostate sample

source_name: Prostectomy 3_tumour prostate sample

value: Prostectomy 3


title: Case1_8

description: normal prostate sample

source_name: Prostectomy 3_normal prostate sample


title: Case1_4

description: normal prostate sample


title: Case4_4

description: normal prostate sample


title: PSP, histologically confirmed diagnose, case 220

value: progressive supranuclear palsy (PSP)

value: case 220


title: PSP, histologically confirmed diagnose, case 219

value: case 219


title: PSP, histologically confirmed diagnose, case 218

value: case 218


title: PSP, histologically confirmed diagnose, case 221

value: case 221


title: Case6_3

description: normal prostate sample

value: Male

value: Normal


title: Case1_3

description: normal prostate sample


title: Case6_1

description: normal prostate sample


title: Case2_1

description: normal prostate sample

value: Prostectomy 7


title: Case6_7

description: normal prostate sample


title: PSP, histologically confirmed diagnose, case 216

value: histologically confirmed diagnose

value: case 216


title: Case1_7

description: normal prostate sample


title: Case4_1

description: tumour prostate sample

value: Prostectomy 9

value: Tumour


title: PSP, histologically confirmed diagnose, case 217

value: case 217

value: frontal cortex, post mortem tissue

value: bisulfite converted DNA from brain tissue


title: PSP, histologically confirmed diagnose, case 214

value: case 214

value: female


title: PSP, histologically confirmed diagnose, case 209

value: progressive supranuclear palsy (PSP)

value: case 209

value: male


title: Case1_5

description: tumour prostate sample

value: Prostectomy 3


title: PSP, histologically confirmed diagnose, case 208

value: case 208


title: Case4_3

description: tumour prostate sample

value: Male


title: PSP, histologically confirmed diagnose, case 213

value: case 213


title: PSP, histologically confirmed diagnose, case 207

value: case 207


title: PSP, histologically confirmed diagnose, case 212

value: histologically confirmed diagnose

value: case 212


title: Case6_4

description: normal prostate sample

value: Prostectomy 5

value: Normal


title: PSP, histologically confirmed diagnose, case 206

value: case 206


title: PSP, histologically confirmed diagnose, case 205

value: case 205

value: frontal cortex, post mortem tissue


title: PSP, histologically confirmed diagnose, case 210

value: case 210

value: bisulfite converted DNA from brain tissue


title: PSP, histologically confirmed diagnose, case 203

value: progressive supranuclear palsy (PSP)

value: case 203

value: female


title: Case2_6

description: tumour prostate sample

value: Prostectomy 7

value: Tumour


title: PSP, histologically confirmed diagnose, case 215

value: case 215


title: PSP, histologically confirmed diagnose, case 201

value: case 201

value: male


title: PSP, histologically confirmed diagnose, case 200

value: histologically confirmed diagnose

value: case 200


title: 43382: tubulovillous adenoma of Patient 41627

city: Beerse

first: Joke

last: Reumers

address: Turnhoutseweg 32

department: DPDS

country: Belgium

institute: Janssen R&D

hyb_protocol: According to the Affymetrix standard protocol (GeneChip3′ IVT Express Kit)

data_processing: Data were analyzed using Bioconductor 3.2 running on R 3.2.2. Probeset expression measures were calculated using the Affymetrix package’s Robust Multichip Average (RMA) default method.

source_name: Patient 41627

extract_protocol: Qiagen RNAeasy FFPE

tag: patient id

value: colorectal adenoma

tag: adenomadiagnosis

value: tubulovillous adenoma


title: 43633: tubulovillous adenoma of Patient 41626

scan_protocol: According to the Affymetrix standard protocol (GeneChip3′ IVT Express Kit)

source_name: Patient 41626

tag: age


title: PSP, histologically confirmed diagnose, case 202

value: case 202


title: Case3_5

description: normal prostate sample

source_name: Prostectomy 2_normal prostate sample

value: Male

value: Prostectomy 2

value: Normal


title: Null-3-16h-Doxo_4

city: Concepción

first: Carlos

last: Farkas

state: Biobío

address: Chacabuco 1140, 1808

department: Bioquímica y Biología Molecular

country: Chile

institute: Universidad de Concepción (UDEC)

description: mRNA depleted of rRNA

data_processing:
Base calling and quality scoring were performed with the Real-Time Analysis system (RTA v2)
Sequenced reads were trimmed for adaptor sequence and then mapped to mm10 whole genome using HISAT2 v2.1.0 (default settings) in the Main Galaxy Platform (https://usegalaxy.org/).
Variant calling was perfomed in every sample using the freebayes parallel script : freebayes-parallel <(fasta_generate_regions.py mm10.fai 100000) 40 -f mm10 -b *.sorted.bam > *.sorted.bam.vcf, where * correspond to WT or KO samples (see https://github.com/ekg/freebayes/blob/master/scripts/freebayes-parallel).
Gene counts per sample were obtained with the HTSeq count script (v0.9.1) implemented in the Galaxy platform against mm10 build. Count Table was constructed in R and normalized with the RUVSeq code (see https://bioconductor.org/packages/release/bioc/html/RUVSeq.html). Differential expression was tested with the edgeRun code in R (see https://cran.r-project.org/web/packages/edgeRun/index.html) between WT and KO samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with gene counts per sample.

source_name: Mouse Embryonic Fibroblasts

growth_protocol: DMEM supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, GE Healthcare HyClone), 1% glutamine (Invitrogen), and 0.5% penicillin/streptomycin (Invitrogen)

extract_protocol:
Total RNA was extracted from each sample with the RNeasy Plus Mini Kit (Qiagen) according to manufacturer's instructions
RNA-Seq libraries were prepared at University of Cambridge sequencing facility (UK) using the TruSeq Stranded mRNA LT Sample Prep Kit (Catalog IDs: RS-122-2101, RS-122-2102). 4 µg of total RNA per sample was depleted of rRNA with the Ribo-Zero Gold rRNA Removal Kit (Illumina) and messenger RNA was further enriched with the Truseq Stranded mRNA Sample Preparation Kit (Illumina). All samples (10) were sequenced using the NextSeq 500 machine with high output configuration (400 million reads, 1x150 bp)

treatment_protocol: Doxorubicin 1 µM (Sigma Aldrich) for sixteen hours

value: Primary MEFs 13.5 days post coitum

tag: passages

value: three

tag: strain

value: Mixed C57BL/6J-129P2OlaHsd


title: Null-3-16h-Doxo_3

description: mRNA depleted of rRNA


title: 43645: serrated adenoma of Patient 41628

source_name: Patient 41628

label_protocol: According to the Affymetrix standard protocol (GeneChip3′ IVT Express Kit)

value: female

tag: tissue

value: serrated adenoma


title: 43386: adenomatous polyp of Patient 41632

source_name: Patient 41632

value: adenomatous polyp


title: Case6_5

description: tumour prostate sample

source_name: Prostectomy 5_tumour prostate sample

value: Prostectomy 5

value: Tumour


title: 43377: tubulovillous adenoma of Patient 41631

source_name: Patient 41631

value: male


title: Case3_4

description: normal prostate sample


title: Case3_3

description: normal prostate sample


title: Null-3-16h-Doxo_2

description: mRNA depleted of rRNA


title: Null-3-16h-Doxo_1

description: mRNA depleted of rRNA


title: Case5_7

description: tumour prostate sample

source_name: Prostectomy 1_tumour prostate sample

value: Prostectomy 1


title: Null-3-Control_3

description: mRNA depleted of rRNA


title: Null-3-Control_4

description: mRNA depleted of rRNA


title: 43356: adenomatous polyp of Patient 41633

source_name: Patient 41633


title: control, no neuronal degeneration post mortem, B97

source_name: control_frontal cortex, post mortem tissue

tag: subject group

value: control

tag: subject status

value: no neuronal degeneration post mortem

value: frontal cortex, post mortem tissue

value: bisulfite converted DNA from brain tissue


title: control, no neuronal degeneration post mortem, B98

tag: subject id


title: Case5_8

description: normal prostate sample

source_name: Prostectomy 1_normal prostate sample

value: Male


title: Null-3-Control_2

description: mRNA depleted of rRNA

tag: cell type


title: Case1_2

description: tumour prostate sample

value: Prostectomy 3


title: PSP, histologically confirmed diagnose, case 204

source_name: PSP_frontal cortex, post mortem tissue

value: progressive supranuclear palsy (PSP)

value: histologically confirmed diagnose

value: case 204


title: Null-3-Control_1

description: mRNA depleted of rRNA

value: Primary MEFs 13.5 days post coitum

value: three

value: Mixed C57BL/6J-129P2OlaHsd


title: control, no neuronal degeneration post mortem, B95

value: female


title: 43410: tubular adenoma of Patient 41634

source_name: Patient 41634

value: colorectal adenoma

value: tubular adenoma


title: Case3_2

description: tumour prostate sample

source_name: Prostectomy 2_tumour prostate sample

value: Prostectomy 2

value: Tumour


title: 43423: adenomatous polyp of Patient 41635

source_name: Patient 41635

value: male

value: adenomatous polyp


title: control, no neuronal degeneration post mortem, B96

value: control

value: no neuronal degeneration post mortem

value: frontal cortex, post mortem tissue


title: 43655: tubulovillous polyp of Patient 41636

source_name: Patient 41636

value: tubulovillous polyp


title: control, no neuronal degeneration post mortem, B94

value: bisulfite converted DNA from brain tissue


title: Case5_4

description: normal prostate sample

value: Male

value: Prostectomy 1

value: Normal


title: Case5_3

description: tumour prostate sample


title: Het-1-16h-Doxo_2

description: mRNA depleted of rRNA

value: Primary MEFs 13.5 days post coitum

value: three


title: Het-1-16h-Doxo_4

description: mRNA depleted of rRNA

value: Mixed C57BL/6J-129P2OlaHsd


title: 43427: tubular adenoma of Patient 41629

source_name: Patient 41629

value: female

value: colorectal adenoma


title: Het-1-16h-Doxo_3

description: mRNA depleted of rRNA


title: 43430: tubulovillous adenoma of Patient 41638

source_name: Patient 41638

value: tubulovillous adenoma


title: 43411: tubulovillous adenoma of Patient 41637

source_name: Patient 41637


title: Case5_1

description: normal prostate sample


title: Case1_1

description: tumour prostate sample

source_name: Prostectomy 3_tumour prostate sample

value: Prostectomy 3

value: Tumour


title: control, no neuronal degeneration post mortem, B92

value: male


title: control, no neuronal degeneration post mortem, B90

value: control


title: control, no neuronal degeneration post mortem, B93

value: no neuronal degeneration post mortem


title: Het-1-16h-Doxo_1

description: mRNA depleted of rRNA

source_name: Mouse Embryonic Fibroblasts


title: control, no neuronal degeneration post mortem, B91

value: frontal cortex, post mortem tissue


title: 43353: tubulovillous adenoma of Patient 41639

source_name: Patient 41639


title: Case5_2

description: normal prostate sample


title: control, no neuronal degeneration post mortem, B89


title: Het-1-Control_4

description: mRNA depleted of rRNA


title: 43716: adenovillous polyp of Patient 41640

source_name: Patient 41640

value: adenovillous polyp


title: PSP, histologically confirmed diagnose, case 211

value: progressive supranuclear palsy (PSP)

value: histologically confirmed diagnose

value: case 211

value: bisulfite converted DNA from brain tissue


title: Het-1-Control_3

description: mRNA depleted of rRNA

value: Primary MEFs 13.5 days post coitum


title: Case5_6

description: normal prostate sample

value: Male

value: Prostectomy 1

value: Normal


title: control, no neuronal degeneration post mortem, B88


title: 43639: tubulovillous adenoma of Patient 41641

source_name: Patient 41641

value: colorectal adenoma


title: Het-1-Control_2

description: mRNA depleted of rRNA

value: three

value: Mixed C57BL/6J-129P2OlaHsd


title: Case3_1

description: tumour prostate sample

value: Prostectomy 2

value: Tumour


title: Het-1-Control_1

description: mRNA depleted of rRNA


title: control, no neuronal degeneration post mortem, B86

value: control

value: male


title: 43349: tubulovillous adenoma of Patient 41645

source_name: Patient 41645

value: female

value: tubulovillous adenoma


title: control, no neuronal degeneration post mortem, B84

value: no neuronal degeneration post mortem

value: frontal cortex, post mortem tissue


title: 43434: adenomatous polyp of Patient 41643

source_name: Patient 41643

value: adenomatous polyp


title: Wild-type-1-16h-Doxo_2

description: mRNA depleted of rRNA


title: 43387: villous adenoma of Patient 41646

source_name: Patient 41646

value: villous adenoma


title: 43653: tubulovillous adenoma of Patient 41648

source_name: Patient 41648


title: Wild-type-1-16h-Doxo_4

description: mRNA depleted of rRNA

value: Primary MEFs 13.5 days post coitum


title: control, no neuronal degeneration post mortem, B83

source_name: control_frontal cortex, post mortem tissue

value: bisulfite converted DNA from brain tissue


title: Wild-type-1-16h-Doxo_3

description: mRNA depleted of rRNA


title: Wild-type-1-16h-Doxo_1

description: mRNA depleted of rRNA


title: Wild-type-1-Control_4

description: mRNA depleted of rRNA


title: control, no neuronal degeneration post mortem, B81


title: control, no neuronal degeneration post mortem, B82


title: control, no neuronal degeneration post mortem, B87


title: Mock [MethylC-seq]

city: Madrid

first: Virginia

last: Ruiz-Ferrer

state: Madrid

address: Ramiro de Maeztu, 9

department: Environmental Biology

country: Spain

institute: CSIC

data_processing:
Data  filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads by using BGI programs (Liang et al., 2014)
Clean data were aligned to the reference genome TAIR10 by BSMAP with the following parameters: bsmap -a filename_1.clean.fq.gz -b filename_2.clean.fq.gz -o filename.sam -d ref.fa -u -v -z 33 -p 4 n0 -w 20 -s 16 -f 10 -L 90
DMR were identified by comparison of the sample1 and sample2 methylomes using windows that contained at least 5CpG (CHG or CHH) sites with a 2-fold change in methylation level and Fisher test p value <= 0.05.
The degree of difference of a methyl-cytosine (mCG, mCHG, mCHH) between samples was calculated by comparing methylation level of DRM of sample1 and sample2 by CIRCOS.
Genome_build: TAIR 10 Arabidosis thaliana genome
Supplementary_files_format_and_content: Mapping Rate: Mapping_Rate.xls
Supplementary_files_format_and_content: Table 1_mC abundance: Abundance of methylated cytosines in the three possible contexts in TRV-infected and mock-inoculated Arabidopsis inflorescences at 14 dpi.
Supplementary_files_format_and_content: Table 2_genome wide mC: Average genome-wide methylation levels of coding genes at the three possible cytosine contexts
Supplementary_files_format_and_content: Table 3_DMRs: Identification of differentially methylated regions (DMR) in which DNA methylation levels varied significantly between TRV-infected and mock-inoculated Arabidopsis inflorescences at 14 dpi.

source_name: inflorescences

growth_protocol: Arabidopsis thaliana plants were grown in controlled environment chambers under 16 h/8 h of light/dark at 22ºC

extract_protocol:
Arabidopsis inflorescences were collected at 14dpi and frozen on liquid nitrogen and genomic DNA (gDNA) was extracted using DNeasy Plant Mini kit (Qiagen).  For mock-samples, the same procedure was performed at 6-weeks-old Arabidopsis plants.
Library construction and Whole Genome Bisulphite sequencing (WGBS) were done by BGI-Tech on Illumina HiSeq2000

treatment_protocol: Arabidopsis plants were inoculated on rosette leaves using fresh inoculum prepared from Nicotiana benthamiana leaves systemically infected with an infectious TRV-GFP clone

tag: ecotype

value: Inflorescences

tag: agent


title: TRV

data_processing:
Illumina GA Pipeline v15 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then used BWA to map clean reads to Arabidopsis genome (TAIR 10) and used Bowtie to gene reference.
FPKM were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR 10 Arabidopsis genome
Supplementary_files_format_and_content: Chepelev et al., Nucleic Acids Research, 2009
Supplementary_files_format_and_content: Clean Data Assess
Supplementary_files_format_and_content: Mapping Assess
Supplementary_files_format_and_content: all.gene.FPKM.xls

growth_protocol: Arabidopsis thaliana plants were were grown in controlled environment chambers under 16 h/8 h of light/dark at 22ºC

extract_protocol:
Inflorescences were collected at 14dpi and frozen on liquid nitrogen, and total RNA was extracted using Trizol reagent. For mock-samples, the same procedure was performed at 6-weeks-old Arabidopsis plants.
Library construction and Illumina sequencing using HiSeq2000 were done by BGI-Tech (Pipeline version 5.0).

value: 6-weeks-old (14dpi)

value: Tobacco rattle virus


title: TRV [MethylC-seq]


title: control, no neuronal degeneration post mortem, B80

extract_protocol: genomic DNA was extracted and purified from post-mortem brain samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

tag: age at death


title: control, no neuronal degeneration post mortem, B85

tag: tssue

tag: molecule subtype


title: Wild-type-1-Control_3

description: mRNA depleted of rRNA

value: three


title: 43420: tubulovillous adenoma of Patient 41650

source_name: Patient 41650

value: colorectal adenoma


title: Wild-type-1-Control_2

description: mRNA depleted of rRNA

value: Mixed C57BL/6J-129P2OlaHsd


title: Wild-type-1-Control_1

description: mRNA depleted of rRNA


title: control, no neuronal degeneration post mortem, B79


title: 43345: adenomatous polyp of Patient 41652

source_name: Patient 41652


title: 43648: tubulovillous adenoma of Patient 41651

source_name: Patient 41651


title: 43704: tubular adenoma of Patient 41653

source_name: Patient 41653

value: tubular adenoma


title: Mock


title: control, no neuronal degeneration post mortem, B78

value: control


title: 43650: tubulovillous polyp of Patient 41649

source_name: Patient 41649

value: tubulovillous polyp


title: control, no neuronal degeneration post mortem, B99

value: male


title: 43370: tubulovillous adenoma of Patient 41654

source_name: Patient 41654

value: tubulovillous adenoma


title: 43409: tubulovillous adenoma of Patient 41656

source_name: Patient 41656


title: 43698: tubulovillous adenoma of Patient 41655

source_name: Patient 41655


title: control, no neuronal degeneration post mortem, B77

value: no neuronal degeneration post mortem


title: Null-2-16h-Doxo_3

description: mRNA depleted of rRNA

source_name: Mouse Embryonic Fibroblasts


title: Null-2-16h-Doxo_2

description: mRNA depleted of rRNA


title: LHX9_rep2

first: Seav Huong

last: Ly

state: MA

address: 450 Brookline Avenue Dana 1511

institute: Harvard University

data_processing:
HiSeq-2500 software was used for basecalling
Sequenced reads were mapped human transcriptome hg19 using TopHat 2.0.2 module
Transcripts were assembled and tested for abundance using Cufflinks 2.0.2 module
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM value for each sample

source_name: colon

growth_protocol: RPMI-1640 media supplemented with 10% FBS and 1% pennicilin and streptinomycin

extract_protocol:
RNA was extracted using PerfectPure RNA Cultured Cell Kit
KAPA RNA-seq library preparation kit (KAPA #KR0934) with NEB index primers (NEB #E6609S)

treatment_protocol: Cells were treated with media or 1ug/mL of doxycycline to induce expression of shKRAS

tag: cell line

value: colon

tag: disease

value: colorectal carcinoma

tag: genetic perturbation

value: Expressing LHX9 open reading frame


title: LHX9_shKRAS_rep2

value: Expressing LHX9 open reading frame and shKRAS


title: Null-2-16h-Doxo_1

description: mRNA depleted of rRNA

value: Primary MEFs 13.5 days post coitum


title: 43416: adenovillous polyp of Patient 41657

source_name: Patient 41657

tag: patient id

tag: age

value: female

tag: adenomadiagnosis

value: adenovillous polyp


title: control, no neuronal degeneration post mortem, B74

value: frontal cortex, post mortem tissue

value: bisulfite converted DNA from brain tissue


title: LHX9_rep1

tag: tissue


title: Null-2-Control_3

description: mRNA depleted of rRNA

tag: passages

value: three

tag: strain


title: 43647: tubulovillous adenoma of Patient 41658

source_name: Patient 41658

value: colorectal adenoma


title: Null-2-Control_4

description: mRNA depleted of rRNA

value: Mixed C57BL/6J-129P2OlaHsd


title: control, no neuronal degeneration post mortem, B72

tag: subject group

value: control

tag: subject status

tag: subject id


title: control, no neuronal degeneration post mortem, B73


title: LacZ_rep2

value: Expressing LacZ open reading frame


title: Null-2-16h-Doxo_4

description: mRNA depleted of rRNA

tag: cell type


title: control, no neuronal degeneration post mortem, B76

tag: gender


title: Null-2-Control_2

description: mRNA depleted of rRNA


title: control, no neuronal degeneration post mortem, B71

tag: age at death


title: control, no neuronal degeneration post mortem, B75

value: male

tag: tssue


title: LacZ_rep1


title: 43649: adenomatous polyp of Patient 41661

source_name: Patient 41661

value: adenomatous polyp


title: 43371: adenomatous polyp of Patient 41659

source_name: Patient 41659


title: 43440: tubular adenoma of Patient 41660

source_name: Patient 41660

value: tubular adenoma


title: Null-2-Control_1

description: mRNA depleted of rRNA


title: Case5_5

description: tumour prostate sample

source_name: Prostectomy 1_tumour prostate sample

value: Male

tag: sample type

value: Prostectomy 1

tag: disease state

value: Tumour


title: 43417: tubulovillous adenoma of Patient 41663

source_name: Patient 41663

value: tubulovillous adenoma


title: control, no neuronal degeneration post mortem, B70

source_name: control_frontal cortex, post mortem tissue

value: no neuronal degeneration post mortem

tag: molecule subtype


title: 43435: tubulovillous adenoma of Patient 41664

source_name: Patient 41664


title: KRAS-G13D_shKRAS_ rep2

tag: cell line

value: colon

tag: disease

value: colorectal carcinoma

tag: genetic perturbation

value: Expressing KRAS-G13D open reading frame and shKRAS


title: LacZ_shKRAS_rep2

value: Expressing LacZ open reading frame and shKRAS


title: Null-1-16h-Doxo_3

description: mRNA depleted of rRNA

value: Primary MEFs 13.5 days post coitum

value: three


title: control, no neuronal degeneration post mortem, B69

value: frontal cortex, post mortem tissue

value: bisulfite converted DNA from brain tissue


title: LacZ_shKRAS_rep1


title: KRAS-G13D_shKRAS_ rep1


title: LHX9_shKRAS_rep1

value: Expressing LHX9 open reading frame and shKRAS


title: control, no neuronal degeneration post mortem, B68

value: control

value: male


title: Null-1-16h-Doxo_1

description: mRNA depleted of rRNA

value: Mixed C57BL/6J-129P2OlaHsd


title: KRAS-G13D_ rep2

value: Expressing KRAS-G13D open reading frame


title: Null-1-Control_4

description: mRNA depleted of rRNA


title: KRAS-G13D_ rep1


title: control, no neuronal degeneration post mortem, B67


title: control, no neuronal degeneration post mortem, B66


title: Null-1-16h-Doxo_4

description: mRNA depleted of rRNA


title: Null-1-Control_3

description: mRNA depleted of rRNA


title: 43376: tubulovillous adenoma of Patient 41666

source_name: Patient 41666

tag: patient id

tag: age

value: female

value: colorectal adenoma

tag: adenomadiagnosis


title: Null-1-Control_2

description: mRNA depleted of rRNA

tag: passages

tag: strain


title: control, no neuronal degeneration post mortem, B65

tag: subject group

tag: subject status