title: BLC_73

city: Paris Cedex 05

first: Cecile

last: Laurent

address: 26 rue d'ulm

institute: Institut Curie

hyb_protocol: Following fragmentation, 10 ug of labelled cRNA were hybridized for 16 hr on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip GCS3000 scanner.

data_processing: Raw data were controlled using Genechip Operating Software and Affymetrix MAS5 algorithm to control the quality of hybridization and synthesis steps. Raw data were analysed using R/Bioconductor and normalized by RMA method.

label: Biotin

source_name: Breast

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix two round amplification  protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. A cleanup with RNAII Nucleospin was conducted according Macherey Nagel recommendations

tag: disease state

value: non medullary basal-like breast carcinoma


title: Metformin_rep2

status: Public on Jun 21 2018

type: RNA

city: Beijing

first: Yuan

last: Zhou

address: 38 Xueyuan Rd, Haidian District

department: Department of Biomedical Informatics and Department of Physiology and Pathophysiology, School of Basic Medical Sciences

country: China

institute: Peking University

hyb_protocol: The microarray hybridization was performed following the standard Agilent pipeline.

scan_protocol: Array slides were scanned using Agilent G2565CA Microarray Scanner.

data_processing: Agilent Feature Extraction software (version 10.7) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX software package (Agilent Technologies).

molecule: total RNA

organism: Mus musculus

source_name: Metformin treated (high fat diet), replicate 2

label_protocol: High quality RNA samples were Cy3 labeled by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio).

growth_protocol: Male 3-week-old C57BL/6J mice (18-21 g) were provided by the Spfanimals Company (Beijing, China). The mice were kept in a temperature- and humidity-controlled (20-24°C, 45-55% humidity) environment with free access to food and water. The protocol was approved by the Beijing Hopital Animal Ethics Committee.

extract_protocol: Total 15 mg of liver tissue was collected and flash frozen by liquid nitrogen. Then the total RNA was extracted by using the Trizol (Invitrogen, USA) following the manufacturer's recommendations. 5μg total RNA was digested with 2μL RNase R 10X Reaction Buffer and 0.5 μL RNase R (10U) for 30 minutes to eliminate linear RNAs.

treatment_protocol: The mice were separated into three groups and treated with different diet and drug. Control group: 17 weeks of normal chow; High fat diet group: 17 weeks of high fat diet chow, and intragastrically treated with saline vehicle for the last 5 weeks; Metformin treated group: 17 weeks of high fat diet chow, and intragastrically treated with 3 mg/kg/day metformin for the last 5 weeks.

tag: tissue

value: liver

tag: gender

value: male

tag: age

value: 20 weeks

tag: strain

tag: diet

value: metformin


title: BLC_78

status: Public on Jun 20 2018

country: France

organism: Homo sapiens


title: BLC_79


title: BLC_74


title: WGS Glioblastoma patient pat_027 Surg.1 frozen [pat_027_N879_12_fv_WGS]

type: SRA

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

library_source: genomic

data_processing:
library strategy: WGS
Low-coverage whole genome sequencing reads were aligned to human reference genome (GRCh38) using BWA’s (v0.7.12) aln and samse commands
Samtools (v1.4) was used for sorting and indexing the aligned short reads.
Copy number aberrations were detected with CNVkit (v0.9.1). This analysis relied on generating expected read counts in each genomic window (~50,000bp) from a set of normal samples and calcu-lating the log2 ratios of the read counts from the tumor samples relative to the normal samples. We used 20 whole genome samples from the Genome Austria project (http://www.personalgenomes.org/at) to generate expected normal/germline read counts for each genomic window. In order to make the high-coverage Genome Austria data comparable with the low-coverage tumor data, we down-sampled them to 36 million reads with 50 basepair read length.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing segmented log2-ratios.

molecule: genomic DNA

source_name: brain (tumor)

extract_protocol:
DNA samples were isolated from fresh-frozen tumor samples using the AllPrep DNA/RNA Mini Kit (Qiagen) following manufacturer’s instructions.
Concentration and fragmentation of DNA extracted from fresh-frozen tumor tissue were assessed with the Qubit 2.0 fluorometric quantitation system (Life Technologies) and agarose gel electrophoresis, respectively. One sample with an insufficiently low DNA concentration was excluded. Libraries were prepared from 1 µg input material using the TruSeq DNA PCR-Free HT Library Prep Kit (Illumina) with IDT for Illumina TruSeq UD Indexes (Integrated DNA Technologies). Briefly, genomic DNA was sheared using a Covaris S220 focused-ultrasonicator instrument, DNA fragments were cleaned, end-repaired, and 3’ A-tailed, followed by ligation of the sequencing adapters. After quality control, individual libraries were diluted, equimolarly pooled, and sequenced on Illumina HiSeq 3000/4000 machines using the 50 basepair single-read setup.

tag: idh status

value: wildtype

tag: center

value: MedUni Vienna

tag: sample group

value: Glioblastoma patient

tag: surgery number

tag: multisector

value: No

tag: sample type

value: frozen


title: TPN_2


title: BLC_70


title: WGS Glioblastoma patient pat_021 Surg.2 frozen [pat_021_N838_13_fv_WGS]


title: BLC_69


title: BLC_64


title: BLC_71


title: WGS Glioblastoma patient ind_43 Surg.NA frozen [ind_43_N656_15_fv_WGS]


title: BLC_66


title: BLC_68


title: BLC_62


title: BLC_60


title: BLC_57


title: BLC_65


title: WGS Glioblastoma patient ind_133 Surg.NA frozen [ind_133_N779_12_fv_WGS]


title: WGS Glioblastoma patient ind_32 Surg.NA frozen [ind_32_N1575_12_fv_WGS]


title: BLC_63


title: BLC_61


title: BLC_58


title: BLC_55


title: BLC_56


title: RNA Glioblastoma patient pat_337 Surg.1 frozen [pat_337_N940_16_fv_RNA]

library_source: transcriptomic

data_processing:
Trimming of adapter sequences was performed with trimmomatic (v0.32). Only reads with a mini-mum length of 25 basepairs after adapter trimming were included in the downstream analysis.
Alignment of the trimmed reads to the human transcriptome (GRCh38 including ncRNAs, Ensembl release 83) was performed with Bowtie1 (v1.1), recording up to 100 different mapping positions for each read (taking into account that one read might originate from any of the different transcripts of one gene).
Calculation of normalized transcript-wise expression estimates (RPKM values) was performed based on the transcriptome alignments using the R package BitSeq (v1.14.0). In order to correct for potential biases in the read distribution, the BitSeq function getExpression() was run with the “uniform” option disabled.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing transcript-wise RPKM values.

molecule: polyA RNA

extract_protocol:
RNA samples were isolated from fresh-frozen tumor samples using the AllPrep DNA/RNA Mini Kit (Qiagen) following manufacturer’s instructions.
Concentration of total RNA extracted from fresh-frozen tissue material was measured using the Qubit 2.0 fluorometric quantitation system (Life Technologies), and the quality was assessed by determining the RNA integrity number (RIN) with an Experion automated electrophoresis system (Bio-Rad). Sam-ples with a RIN score below 5 (7 samples) were excluded. Libraries for transcriptome profiling were prepared from a target amount of 1 µg input RNA with the TruSeq Stranded mRNA LT sample prepa-ration kit (Illumina) using Sciclone and Zephyr liquid handling workstations (PerkinElmer). Final li-brary concentrations were quantified with the Qubit 2.0 fluorometric quantitation system, and the fragment size distribution was assessed using the Experion automated electrophoresis System. Individ-ual libraries were diluted and pooled equimolarly, followed by sequencing on Illumina HiSeq 3000/4000 machines using the 50 basepair single-read setup.


title: BLC_52


title: RNA Glioblastoma patient pat_336 Surg.1 frozen [pat_336_N724_16_fv_RNA]


title: RNA Glioblastoma patient pat_333 Surg.1 frozen [pat_333_N2712_15_fv_RNA]


title: TPN_1


title: RNA Glioblastoma patient pat_332 Surg.1 frozen [pat_332_N255_16_fv_RNA]


title: RNA Glioblastoma patient pat_330 Surg.1 frozen [pat_330_N1298_16_fv_RNA]


title: RNA Glioblastoma patient pat_187 Surg.1 frozen [pat_187_N2611_14_fv_RNA]


title: RNA Glioblastoma patient pat_331 Surg.1 frozen [pat_331_N1835_16_fv_RNA]


title: RNA Glioblastoma patient pat_184 Surg.1 frozen [pat_184_N1390_13_fv_RNA]


title: BLC_50


title: RNA Glioblastoma patient pat_183 Surg.1 frozen [pat_183_N922_12_fv_RNA]


title: RNA Glioblastoma patient pat_334 Surg.1 frozen [pat_334_N570_16_fv_RNA]


title: BLC_40


title: BLC_37


title: BLC_39


title: RNA Glioblastoma patient pat_173 Surg.1 frozen [pat_173_N337_13_fv_RNA]


title: RNA Glioblastoma patient pat_180 Surg.1 frozen [pat_180_N560_12_fv_RNA]


title: BLC_33


title: RNA Glioblastoma patient pat_165 Surg.1 frozen [pat_165_N592_15_fv_RNA]


title: RNA Glioblastoma patient pat_164 Surg.1 frozen [pat_164_N581_14A_fv_RNA]


title: RNA Glioblastoma patient pat_163 Surg.1 frozen [pat_163_N541_15_fv_RNA]


title: BLC_38


title: BLC_36


title: RNA Glioblastoma patient pat_157 Surg.1 frozen [pat_157_N2085_14B_fv_RNA]


title: BLC_35


title: RNA Glioblastoma patient pat_155 Surg.1 frozen [pat_155_N1883_14_fv_RNA]


title: RNA Glioblastoma patient pat_153 Surg.1 frozen [pat_153_N1672_14_fv_RNA]


title: MBC43

value: medullary breast carcinoma


title: RNA Glioblastoma patient pat_151 Surg.1 frozen [pat_151_N1543_14E_fv_RNA]


title: Control_rep1

source_name: Control (chow diet), replicate 1

value: control


title: RNA Glioblastoma patient pat_147 Surg.1 frozen [pat_147_N1436_15_fv_RNA]


title: MBC42


title: MBC12


title: RNA Glioblastoma patient pat_146 Surg.1 frozen [pat_146_N1383_14A_fv_RNA]


title: MBC44


title: BLC_31


title: BLC_32


title: BLC_30


title: MBC11


title: RNA Glioblastoma patient pat_143 Surg.1 frozen [pat_143_N1160_15_fv_RNA]


title: MBC05


title: MBC03


title: MBC01


title: RNA Glioblastoma patient pat_140 Surg.1 frozen [pat_140_N2207_13_fv_RNA]


title: MBC04


title: MBC13


title: RNA Glioblastoma patient pat_150 Surg.1 frozen [pat_150_N1541_14_fv_RNA]


title: RNA Glioblastoma patient pat_136 Surg.1 frozen [pat_136_N1290_12_fv_RNA]


title: RNA Glioblastoma patient pat_121 Surg.1 frozen [pat_121_N2613_14_fv_RNA]


title: RNA Glioblastoma patient pat_169 Surg.1 frozen [pat_169_N579_12_fv_RNA]


title: MBC23


title: RNA Low-grade glioma patient pat_108 Surg.5 frozen [pat_108_N54_13_fv_RNA]

value: mutant

value: Low-grade glioma patient


title: RNA Glioblastoma patient pat_043 Surg.1 frozen [pat_043_N486_13_fv_RNA]


title: MBC07


title: MBC08


title: MBC06


title: GM12878_RepliSeq

city: Pittsburgh

first: Yang

last: Yang

state: PA

address: 5000 Forbes Ave

department: Computational Biology

country: USA

institute: Carnegie Mellon University

description: Files named *.24k.norm.bw are imputed, smoothed and scaled processed data. human.R1.6k.bw is intermediate processed file with non-imputed, non-smoothed and non-scaled data. Human has two replicates R1 and R2. Raw files with ID 1108,1208 are for R2. Raw files with ID 0908, 1008 are for R1. For human only R2 is used for study and has imputed, smoothed and scaled processed data.

data_processing:
Library strategy: RepliSeq
Quality control for fastq files were performed with low quality reads trimed using fastqc.
The adapter sequences were removed using FASTX-Toolkit with parameters fastx_clipper -Q 33 -v -n -l 10. Reads were mapped to hg19 (panTro4,ponAbe2,nomLeu3,chlSab2 respectively, for reads from different species) with Bowtie2.
SAM to BAM format conversion, sorting of BAM file and removal of duplicate reads were performed using Samtools.BAM file was converted to BED file using bamToBed.
The reference genome hg19 were divided into 6kb bins and aligned to the genome of each of the other primate species to the human genome using liftOver, to obtain the orthologous region of each bin in human in the other primate species, with command: liftOver oldFile map.chain newFile unMapped -minMatch=0.5
Read count in each given genome window (orthologous region) was calculated and normalized by the total read count in replication timing (RT) early or late fraction on the whole genome, respectively.
Base 2 logarithm ratio of read count per million reads between the early and late fractions of RT within a genome window was calculated as the original RT signal of this window.
Missing data within gaps smaller than 48kb were imputed using nearest neighbor imputation
RT signals of each species were smoothed with wavelet smoothing using HMMSeg with window size of 24kb.
Orthologous regioins across five species where RT signals of five species are all available are extracted. RT signals in these regions are scaled to be [0,5] for early RT and [-5,0] for late RT for each species.
Genome_build: hg19
Genome_build: panTro4
Genome_build: ponAbe2
Genome_build: nomLeu3
Genome_build: chlSab2
Supplementary_files_format_and_content: bigWig files were generated with the value column represents the RT signal (log2 ratio of read count per million reads between the early and late fractions of RT within the orthologous region).  The region in each file is the aligned region in the reference genome (hg19). human.R1.6k.bw is intermediated processsed file for human replicate 1 of which the RT signals were non-imputed, non-smoothed and non-scaled.

source_name: GM12878 B-lymphocyte

growth_protocol: GM12878 growth condition is described at https://data.4dnucleome.org/biosources/4DNSRH17RFKR/,  https://data.4dnucleome.org/biosamples/4DNBS3I5U7BY/. For the lymphocyte cells of chimpanzee, orangutan, gibbon and green monkey, all suspensions (lymphocytes) were cultured using RPMI,10%FBS,1%P/S,1%Lglut.Cultures were maintained in T25 flasks at 37˚C, 5% CO2 and passaged to maintain adequate confluency.

tag: cell type

value: EBV-transformed B-lymphocyte cell line

tag: cell line


title: RNA Glioblastoma patient pat_103 Surg.2 frozen [pat_103_N1934_14_fv_RNA]


title: RNA Glioblastoma patient pat_134 Surg.1 frozen [pat_134_N466_12A_fv_RNA]


title: RNA Glioblastoma patient pat_021 Surg.2 frozen [pat_021_N838_13_fv_RNA]


title: RNA Glioblastoma patient ind_32 Surg.NA frozen [ind_32_N1575_12_fv_RNA]


title: RRBS Glioblastoma patient pat_337 Surg.1 frozen [pat_337_N940_16_fv]

data_processing:
Adapter sequences were trimmed, and 60 basepair reads were cropped to 50 basepairs using Trimmomatic with the following settings: ILLUMINACLIP:RRBS_adapters.fa:2:40:7 SLIDINGWINDOW:4:15. MAXINFO:20:0.50 CROP:50 MINLEN:18.
Trimmed reads were then aligned to the human genome build hg38 using BSMAP in RRBS mode.
DNA methylation calling was performed with a custom python script (biseqMethCalling.py).
Genome_build: hg38
Supplementary_files_format_and_content: Bed files containing CpG DNA methylation levels

extract_protocol:
Genomic DNA was extracted from FFPE tissues using the QIAamp DNA FFPE Tissue Kit following manufacturer’s instructions
RRBS was performed using 100 ng of genomic DNA for most samples, while occasionally going down to 2 ng (if not more DNA was available) and up to 200 ng. To assess bisulfite conversion efficiency independent of CpG context, methylated and unmethylated spike-in controls were added in a concentration of 0.1%. DNA was digested using the restriction enzymes MspI and Taq1 in combination (as opposed to MspI only in the original protocol) in order to increase genome-wide coverage. Restriction enzyme digestion was followed by fragment end repair, A-tailing, and adapter ligation. The amount of effective library was determined by qPCR, and samples were multiplexed in pools of 10 with similar qPCR Ct values. The pools were then subjected to bisulfite conversion followed by library enrichment by PCR. Enrichment cycles were determined using qPCR and ranged from 12 to 21 (median: 16). Adequate fragment size distributions were confirmed on Bioanalyzer High Sensitivity DNA chips (Agilent).


title: RNA Glioblastoma patient ind_133 Surg.NA frozen [ind_133_N779_12_fv_RNA]


title: RRBS Glioblastoma patient pat_336 Surg.1 frozen [pat_336_N724_16_fv]


title: RRBS Glioblastoma patient pat_334 Surg.1 frozen [pat_334_N570_16_fv]


title: RRBS Glioblastoma patient pat_336 Surg.1 FFPE [pat_336_N727_16]

value: FFPE


title: MBC38


title: MBC36


title: RRBS Glioblastoma patient pat_337 Surg.1 FFPE [pat_337_N940_16]


title: MBC32


title: MBC28


title: RRBS Glioblastoma patient pat_333 Surg.1 frozen [pat_333_N2712_15_fv]


title: MBC30


title: RRBS Glioblastoma patient pat_333 Surg.1 FFPE [pat_333_N2712_15]


title: RNA Glioblastoma patient pat_027 Surg.1 frozen [pat_027_N879_12_fv_RNA]


title: RRBS Glioblastoma patient pat_334 Surg.1 FFPE [pat_334_N570_16]


title: RRBS Glioblastoma patient pat_332 Surg.1 frozen [pat_332_N255_16_fv]


title: RNA Glioblastoma patient pat_027 Surg.2 frozen [pat_027_N1154_13_fv_RNA]


title: RRBS Glioblastoma patient pat_332 Surg.1 FFPE [pat_332_N255_16]


title: RRBS Glioblastoma patient pat_331 Surg.1 FFPE [pat_331_N1835_16]


title: RRBS Glioblastoma patient pat_331 Surg.1 frozen [pat_331_N1835_16_fv]


title: RRBS Glioblastoma patient pat_330 Surg.1 FFPE [pat_330_N1298_16]


title: RRBS Glioblastoma patient pat_266 Surg.1 FFPE [pat_266_Graz_55_1]

value: Graz


title: RNA Glioblastoma patient ind_43 Surg.NA frozen [ind_43_N656_15_fv_RNA]


title: RRBS Glioblastoma patient pat_263 Surg.1 FFPE [pat_263_Graz_52]


title: RRBS Glioblastoma patient pat_265 Surg.1 FFPE [pat_265_Graz_54]


title: RRBS Glioblastoma patient pat_330 Surg.1 frozen [pat_330_N1298_16_fv]


title: RRBS Glioblastoma patient pat_261 Surg.1 FFPE [pat_261_Graz_50_1]


title: RRBS Glioblastoma patient pat_267 Surg.1 FFPE [pat_267_Graz_56_2]


title: RRBS Glioblastoma patient pat_260 Surg.1 FFPE [pat_260_Graz_49_2]


title: RRBS Glioblastoma patient pat_238 Surg.1 FFPE [pat_238_N500_10]


title: WGS Glioblastoma patient pat_027 Surg.2 frozen [pat_027_N1154_13_fv_WGS]


title: RRBS Glioblastoma patient pat_259 Surg.1 FFPE [pat_259_Graz_47]


title: RRBS Glioblastoma patient pat_264 Surg.1 FFPE [pat_264_Graz_53]


title: RRBS Glioblastoma patient pat_268 Surg.1 FFPE [pat_268_Graz_57]


title: RRBS Glioblastoma patient pat_237 Surg.1 FFPE [pat_237_N831_11]


title: RRBS Glioblastoma patient pat_230 Surg.1 FFPE [pat_230_N1254_06A]


title: RRBS Glioblastoma patient pat_231 Surg.1 FFPE [pat_231_N1582_06Z]


title: RRBS Glioblastoma patient pat_226 Surg.1 FFPE [pat_226_N1653_07B]


title: RRBS Glioblastoma patient pat_225 Surg.1 FFPE [pat_225_N144_06]


title: RRBS Glioblastoma patient pat_227 Surg.1 FFPE [pat_227_N1381_07]


title: RRBS Glioblastoma patient pat_222 Surg.1 FFPE [pat_222_N324_08]


title: RRBS Glioblastoma patient pat_232 Surg.1 FFPE [pat_232_N1225_11]


title: RRBS Glioblastoma patient pat_228 Surg.1 FFPE [pat_228_N526_06]


title: RRBS Glioblastoma patient pat_262 Surg.1 FFPE [pat_262_Graz_51_1]


title: RRBS Glioblastoma patient pat_234 Surg.1 FFPE [pat_234_N960_06]


title: RRBS Glioblastoma patient pat_258 Surg.1 FFPE [pat_258_Graz_46_2]


title: RRBS Glioblastoma patient pat_221 Surg.1 FFPE [pat_221_N87_09B]


title: RRBS Glioblastoma patient pat_223 Surg.1 FFPE [pat_223_N724_07]


title: BLC_53

value: non medullary basal-like breast carcinoma


title: RRBS Glioblastoma patient pat_219 Surg.1 FFPE [pat_219_N1509_08]


title: RRBS Glioblastoma patient pat_218 Surg.1 FFPE [pat_218_N711_09]


title: RRBS Glioblastoma patient pat_236 Surg.1 FFPE [pat_236_N7_11]


title: RRBS Glioblastoma patient pat_217 Surg.1 FFPE [pat_217_N1563_09]


title: RRBS Glioblastoma patient pat_216 Surg.1 FFPE [pat_216_N1516_10B]


title: RRBS Glioblastoma patient pat_229 Surg.1 FFPE [pat_229_N1248_06]


title: RRBS Glioblastoma patient pat_213 Surg.1 FFPE [pat_213_N1261_10B]


title: RRBS Glioblastoma patient pat_233 Surg.1 FFPE [pat_233_N435_06]


title: RRBS Glioblastoma patient pat_224 Surg.1 FFPE [pat_224_N1173_07]


title: RRBS Glioblastoma patient pat_211 Surg.1 FFPE [pat_211_N30_13]


title: RRBS Glioblastoma patient pat_199 Surg.1 FFPE [pat_199_N1722_10]


title: RRBS Glioblastoma patient pat_186 Surg.1 FFPE [pat_186_N177_13]


title: RRBS Glioblastoma patient pat_185 Surg.1 FFPE [pat_185_N540_09A]


title: RRBS Glioblastoma patient pat_220 Surg.1 FFPE [pat_220_N567_09C]


title: RRBS Glioblastoma patient pat_187 Surg.1 frozen [pat_187_N2611_14_fv]


title: RRBS Glioblastoma patient pat_210 Surg.1 FFPE [pat_210_N296_09]


title: RRBS Glioblastoma patient pat_183 Surg.1 frozen [pat_183_N922_12_fv]


title: RRBS Glioblastoma patient pat_184 Surg.1 FFPE [pat_184_N1390_13C]


title: RRBS Glioblastoma patient pat_182 Surg.1 FFPE [pat_182_N892_10]


title: RRBS Glioblastoma patient pat_186 Surg.1 frozen [pat_186_N177_13_fv]


title: RRBS Glioblastoma patient pat_181 Surg.1 FFPE [pat_181_N951_09B]


title: RRBS Glioblastoma patient pat_180 Surg.1 frozen [pat_180_N560_12_fv]


title: RRBS Glioblastoma patient pat_180 Surg.1 FFPE [pat_180_N560_12C]


title: MeT-5A-NF2-WT#1

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

country: Japan

institute: Kinjo Gakuin University

description: Gene expression in MeT-5A-NF2-WT#1 cell clone

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2519F-026652) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026652_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Met-5A cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human mesothelium MeT-5A were provided by the ATCC through the American Type Culture Collection , and were grown in RPMI containing 10% fetal bovine serum (FBS) at 37 °C in a 5% CO2 incubator.

extract_protocol: RNA was prepared using RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations. RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Parental MeT-5A and the established cell clones  were plated at 80% confluence and cultured for 16 hours

value: mesothelium

tag: genotype/variation


title: MeT-5A-NF2-KO#2

description: Gene expression in MeT-5A-NF2-KO#2 cell clone

value: male


title: RRBS Glioblastoma patient pat_179 Surg.1 FFPE [pat_179_N2266_13]


title: RRBS Glioblastoma patient pat_177 Surg.1 FFPE [pat_177_N815_08]


title: RRBS Glioblastoma patient pat_178 Surg.1 FFPE [pat_178_N586_12]


title: MeT-5A-NF2-WT#2

description: Gene expression in MeT-5A-NF2-WT#2 cell clone


title: RRBS Glioblastoma patient pat_215 Surg.1 FFPE [pat_215_N1277_10]


title: RRBS Glioblastoma patient pat_198 Surg.1 FFPE [pat_198_N313_10]


title: RRBS Glioblastoma patient pat_176 Surg.1 FFPE [pat_176_N1767_06B]


title: RRBS Glioblastoma patient pat_175 Surg.1 FFPE [pat_175_N1021_08G1]


title: MeT-5A-parent

description: Gene expression in MeT-5A-parental cells

value: MeT-5A-parental cells


title: RRBS Glioblastoma patient pat_187 Surg.1 FFPE [pat_187_N2611_14D]


title: RRBS Glioblastoma patient pat_184 Surg.1 frozen [pat_184_N1390_13_fv]


title: RRBS Glioblastoma patient pat_188 Surg.1 FFPE [pat_188_N2699_14B]


title: MeT-5A-NF2-KO#1

description: Gene expression in MeT-5A-NF2-KO#1 cell clone


title: RRBS Glioblastoma patient pat_173 Surg.1 FFPE [pat_173_N337_13]


title: RRBS Glioblastoma patient pat_173 Surg.1 frozen [pat_173_N337_13_fv]


title: RRBS Glioblastoma patient pat_171 Surg.1 frozen [pat_171_N834_13_fv]


title: RRBS Glioblastoma patient pat_169 Surg.1 frozen [pat_169_N579_12_fv]


title: RRBS Glioblastoma patient pat_171 Surg.1 FFPE [pat_171_N834_13]


title: RRBS Glioblastoma patient pat_174 Surg.1 FFPE [pat_174_N836_09G2]


title: RRBS Glioblastoma patient pat_183 Surg.1 FFPE [pat_183_N922_12A]


title: RRBS Glioblastoma patient pat_172 Surg.1 FFPE [pat_172_N1043_09]


title: RRBS Glioblastoma patient pat_167 Surg.1 FFPE [pat_167_N712_14]


title: RRBS Glioblastoma patient pat_169 Surg.1 FFPE [pat_169_N579_12A]


title: RRBS Glioblastoma patient pat_166 Surg.1 FFPE [pat_166_N697_14]


title: RRBS Glioblastoma patient pat_168 Surg.1 FFPE [pat_168_N900_15B]


title: RRBS Glioblastoma patient pat_165 Surg.1 FFPE [pat_165_N592_15B]


title: RRBS Glioblastoma patient pat_164 Surg.1 FFPE [pat_164_N581_14A]


title: RRBS Glioblastoma patient pat_164 Surg.1 frozen [pat_164_N581_14A_fv]


title: RRBS Glioblastoma patient pat_163 Surg.1 frozen [pat_163_N541_15_fv]


title: RRBS Glioblastoma patient pat_163 Surg.1 FFPE [pat_163_N541_15]


title: RRBS Glioblastoma patient pat_162 Surg.1 FFPE [pat_162_N487_16]


title: RRBS Glioblastoma patient pat_160 Surg.1 FFPE [pat_160_N2606_15]


title: RRBS Glioblastoma patient pat_159 Surg.1 FFPE [pat_159_N2395_15]


title: RRBS Glioblastoma patient pat_161 Surg.1 FFPE [pat_161_N418_14]


title: RRBS Glioblastoma patient pat_158 Surg.1 FFPE [pat_158_N2242_15]


title: RRBS Glioblastoma patient pat_156 Surg.1 FFPE [pat_156_N2012_14]


title: RRBS Glioblastoma patient pat_157 Surg.1 frozen [pat_157_N2085_14B_fv]


title: RRBS Glioblastoma patient pat_165 Surg.1 frozen [pat_165_N592_15_fv]


title: RRBS Glioblastoma patient pat_155 Surg.1 frozen [pat_155_N1883_14_fv]


title: RRBS Glioblastoma patient pat_155 Surg.1 FFPE [pat_155_N1883_14]


title: RRBS Glioblastoma patient pat_154 Surg.1 FFPE [pat_154_N1875_14]


title: Ganglia_E09_rep2

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: Labeled cRNA was hybridized to the Agilent-026441 Gallus gallus (Chicken) v2 Oligo 4×44K Microarray according to the manufacturer's protocol.

scan_protocol: The arrays were scanned with an Agilent Microarray Scanner (G2505C, Agilent Technologies) at 535 nm for Cy3.

data_processing: Signal intensities were calculated using Feature Extraction software (FE, Vers. 10.7.3.1; Agilent Technologies).  Probe signal intensities were background corrected and normalized via the cyclic loess method using the LIMMA package from the R/Bioconductor environment.

organism: Gallus gallus

source_name: Avian ciliary ganglion

label_protocol: 100 ng of total RNA was labeled using LowInputQuick Amp Labeling kit (Agilent 5190-2305) following manufacturer instructions.

extract_protocol: Total RNA was prepared using TotalRNA Easy (Quiagen, Hilden, Germany). RNA integrity numbers  determined with the Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany)

tag: developmental stage

value: Ciliary ganglia


title: Ganglia_E14_rep2


title: Ganglia_E14_rep3


title: RRBS Glioblastoma patient pat_157 Surg.1 FFPE [pat_157_N2085_14B]

value: wildtype


title: RRBS Glioblastoma patient pat_153 Surg.1 frozen [pat_153_N1672_14_fv]

value: MedUni Vienna


title: Ganglia_E14_rep1


title: Ganglia_E10_rep4


title: Ganglia_E08_rep1


title: Ganglia_E07_rep3


title: Ganglia_E10_rep1


title: Ganglia_E14_rep4


title: Ganglia_E07_rep4


title: RRBS Glioblastoma patient pat_152 Surg.1 FFPE [pat_152_N1576_15]

value: Glioblastoma patient


title: Ganglia_E08_rep3


title: Ganglia_E09_rep1


title: Ganglia_E09_rep3


title: Ganglia_E10_rep2


title: RRBS Glioblastoma patient pat_153 Surg.1 FFPE [pat_153_N1672_14]

value: No


title: Ganglia_E08_rep4


title: Ganglia_E10_rep3


title: Ganglia_E09_rep4


title: RRBS Glioblastoma patient pat_151 Surg.1 frozen [pat_151_N1543_14E_fv]

value: frozen


title: RRBS Glioblastoma patient pat_150 Surg.1 frozen [pat_150_N1541_14_fv]


title: Ganglia_E06_rep4


title: Ganglia_E07_rep2


title: RRBS Glioblastoma patient pat_151 Surg.1 FFPE [pat_151_N1543_14E]


title: Ganglia_E07_rep1


title: RRBS Glioblastoma patient pat_149 Surg.1 FFPE [pat_149_N1491_15]


title: Ganglia_E06_rep2


title: RRBS Glioblastoma patient pat_147 Surg.1 frozen [pat_147_N1436_15_fv]


title: 4 µM 7l, 60 min, rep 2

city: Berkeley

first: Jamie

last: Cate

state: CA

address: 748 Stanley Hall

institute: University of California

description:
ribo-seq
Sample 5

data_processing:
Library strategy: ribo-seq
Adapter sequences (CTGTAGGCACCATCAAT) were trimmed and reads were filtered for minimum length using FASTX-clipper version 0.0.13
Ribosomal RNA sequences were computationally removed by aligning the reads to a set of human rRNA sequences with Bowtie version 1.1.2
Nonribosomal sequences from samples 7-9 (vehicle only) were pooled were pseudoaligned to a reference consiting of all transcripts annotated as "Known" and "Protein coding" in the ENSEMBL GRCh38 annotation using Kallisto version 0.42.5 to determine the relative abundance of the transcript isoforms. This was done with python version 3.5.1 .
A custom reference transcriptome consisting of the most abundant transcript isoform from each gene was generated using python version 3.5.1. All Python code is in "Python_code.txt"
Nonribosomal sequences were aligned with the custom transcriptome using Bowtie version 1.1.2
Reads mapping to more then five locations in the custom transcriptome were filtered out using python version 2.7.5. All Python code is in "Python_code.txt"
Readmaps indicating the number of reads alining to each position of the custom transcriptome were genenerated using python 2.7.5. All Python code is in "Python_code.txt"
Metareadmaps" showing the average distribution of reads relative to the start and stop codons for all genes were generated using python version 2.7.5 These maps were used to determine the distance between the 5' end of read alingments and the ribosomal P-site. All Python code is in "Python_code.txt
The readmaps were converted from nucleotide-based to codon-based using python 2.7.5 All Python code is in "Python_code.txt"
The readmaps were normalized from raw reads to reads per million using python 2.7.5. All Python code is in "Python_code.txt"
Cumulative fractional readplots, Dmax values and Dmax positions were calculated using python 2.7.5. All Python code is in "Python_code.txt"
Dmax values were Z-score transformed as described in Andreev et al. (2015) Genome Biology 16:90 using python verson 2.7.5. All Python code is in "Python_code.txt"
For genes with a Dmax Zscore > 2 reads mapping to the CDS 3' to the position of Dmax were extracted for DeSeq analysis. For Dmax Z-score ≤ 2, reads mapping 3' to codon 50 were extracted. In all cases, the 10 3'-most codons were omitted. All Python code is in "Python_code.txt"
Genome_build: Rnor6
Supplementary_files_format_and_content: *codonmap.txt files are plain text files with three columns, the first is the transcript accession number, the second is the codon, relative to start, the third is the number of reads that align to that position based on the infered location of the ribosome P-site.
Supplementary_files_format_and_content: Poststall_Deseq_analyses.xlsx is an Excel spreadsheet with Differential expression analysis that uses the Dmax approach to predict potential stall sites and use only alignments mapping 3' to those sites.
Supplementary_files_format_and_content: Raw_read_counts.xlsx is an Excel speadsheet summarizing raw alignment counts.
Supplementary_files_format_and_content: Python_code.txt is an Text file containing the custom python code used to process the data.
Supplementary_files_format_and_content: Rnor6_protein_coding_cDNAs.fa is the Multifasta file with reference transcriptome used for the initial Kallisto psudoaligments.
Supplementary_files_format_and_content: IEC6_most_abundant_isoforms.fa is the Multifasta file with reference transcriptome of only the most abundant splice isoform from each locus, used in the bowtie alignments.

organism: Rattus norvegicus

source_name: IEC6 cells

growth_protocol: IEC6 cells (ATCVC CRL-1592)  were maintained in DMEM ((Life Technologies 11995-073) supplemented with 10% FBS (Tissue Culture Biologicals Cat # 101) and 1X Insulin-Transferrin-Selenium (Life Technologies 51300-044) at 37 ˚C under a 5% CO2 atmosphere.

extract_protocol:
The cells were harvested by aspiration of media and immediate addition of ice-cold PBS containing 100 µg/mL cycloheximide.  The PBS plus cycloheximide was aspirated with a vacuum aspirator and 800 µL lysis buffer (20 mM Tris-Cl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM dithiothreitol, 100 µg/mL cycloheximide, 1% Triton X-100 and 25 U/mL DNase I (Promega)) was added.
Cells were lysed and ribosome footprint or fragmented RNA libraries were generated as described in Ingolia et al. Curr Protoc Mol Biol Chapter 4, Unit 4 18 (2013).

treatment_protocol: IEC6 cells were grown in 15 cm plates to a confluence of 60-80%.  The cells were always passaged into fresh media within 24 hours of the experiment. The media was replaced with fresh prewarmed media containing 4 µM or7f (PF-06446846), 7l (PF-06649492), or vehicle (0.5% DMSO) and the plates were immediately returned to the incubator for 10 or 60 minutes as indicated.

tag: compound treatment

value: 4 µM 7l

tag: treatment time

value: 60 min


title: 4 µM 7f, 60 min, rep 2

description:
ribo-seq
Sample 2

value: 4 µM 7f


title: 4 µM 7f, 60 min, rep 1

description:
ribo-seq
Sample 1


title: RRBS Glioblastoma patient pat_147 Surg.1 FFPE [pat_147_N1436_15]


title: RRBS Glioblastoma patient pat_145 Surg.1 FFPE [pat_145_N1336_14A]


title: Ganglia_E08_rep2

tag: tissue


title: vehicle, 60 min rep 2

description:
ribo-seq
Sample 8

value: Vehicle


title: vehicle, 60 min rep 3

description:
ribo-seq
Sample 9


title: RRBS Glioblastoma patient pat_146 Surg.1 FFPE [pat_146_N1383_14A]


title: Ganglia_E06_rep3


title: Ganglia_E06_rep1


title: RRBS Glioblastoma patient pat_143 Surg.1 frozen [pat_143_N1160_15_fv]


title: 4 µM 7l, 60 min, rep 3

description:
ribo-seq
Sample 6


title: 4 µM 7f, 60 min, rep 3

description:
ribo-seq
Sample 3


title: RRBS Glioblastoma patient pat_146 Surg.1 frozen [pat_146_N1383_14A_fv]


title: vehicle, 60 min rep 1

description:
ribo-seq
Sample 7


title: RRBS Glioblastoma patient pat_150 Surg.1 FFPE [pat_150_N1541_14]


title: CHD8_mOL

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to rn5 whole genome by Bowtie2 with default options
Use samtools to delete the duplicate reads
Peak calling was performed using MACS1.4 with a default p value cut off.
Genome_build: rn5
Supplementary_files_format_and_content: wig files were generated by MACS14

source_name: rat oligodendrocyte

growth_protocol: Briefly, mixed glial cells were initially cultured in DMEM-F12 medium supplied with 15% FBS, then switched to B104 conditioned medium for 2 days before isolating OPCs by mechanical detachment in an orbital shaker. Isolated rat OPCs were grown in Sato growth medium supplemented with mitogens 10 ng/ml PDGF-AA and 10 ng/ml bFGF, and differentiated in OL Differentiation Medium (Sato medium supplemented with 15 nM T3 and 10 ng/ml ciliary neurotrophic factor).

extract_protocol:
In brief, chromatin was cross-linked and sheared with a Covaris S220 sonicator from primary oligodendrocyte cultures of newborn rat or mouse cortex. Immunoprecipitation was overnight at 4°C using antibodies directed against or control immunoglobulins in the presence of protein A/G Sepharose CL-4B beads (Life Technologies) pretreated with BSA. Rabbit anti-CHD8 (ab114126) antibodies were used for immunoprecipitation. After reverse crosslink, proteinase K treatment, the precipitated chromatin DNA was purified.
libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB cat # E6240L), and then to sequence on the Illumina sequencer HS2500.

value: rat oligodendrocyte


title: RRBS Glioblastoma patient pat_148 Surg.1 FFPE [pat_148_N1448_14]

value: FFPE


title: RRBS Glioblastoma patient pat_142 Surg.1 FFPE [pat_142_N1024_15B]


title: RRBS Glioblastoma patient pat_141 Surg.1 FFPE [pat_141_N1711_10B]


title: RRBS Glioblastoma patient pat_140 Surg.1 frozen [pat_140_N2207_13_fv]


title: RRBS Glioblastoma patient pat_144 Surg.1 FFPE [pat_144_N1236_14A]


title: 4 µM 7l, 60 min, rep 1

description:
ribo-seq
Sample 4


title: CHD8_OPC

source_name: rat OPC

value: rat OPC


title: RRBS Glioblastoma patient pat_140 Surg.1 FFPE [pat_140_N2207_13]


title: RRBS Glioblastoma patient pat_139 Surg.1 frozen [pat_139_N654_12_fv]


title: RRBS Glioblastoma patient pat_139 Surg.1 FFPE [pat_139_N654_12B]


title: RRBS Glioblastoma patient pat_138 Surg.1 FFPE [pat_138_N637_10]


title: RRBS Glioblastoma patient pat_137 Surg.1 FFPE [pat_137_N1351_09B]


title: RRBS Glioblastoma patient pat_134 Surg.1 frozen [pat_134_N466_12A_fv]


title: RRBS Glioblastoma patient pat_135 Surg.1 FFPE [pat_135_N1583_07]


title: RRBS Glioblastoma patient pat_132 Surg.1 FFPE [pat_132_N1581_09B]


title: RRBS Glioblastoma patient pat_136 Surg.1 frozen [pat_136_N1290_12_fv]


title: RRBS Glioblastoma patient pat_136 Surg.1 FFPE [pat_136_N1290_12C]


title: RRBS Glioblastoma patient pat_134 Surg.1 FFPE [pat_134_N466_12A]


title: RRBS Glioblastoma patient pat_131 Surg.1 FFPE [pat_131_N104_11B]


title: RRBS Glioblastoma patient pat_130 Surg.1 FFPE [pat_130_N473_09]


title: RRBS Glioblastoma patient pat_129 Surg.1 FFPE [pat_129_N307_08C]

value: mutant


title: RRBS Glioblastoma patient pat_128 Surg.1 FFPE [pat_128_N661_08G3]


title: RRBS Glioblastoma patient pat_121 Surg.1 frozen [pat_121_N2613_14_fv]


title: Control2

city: Suita

first: Mitsunbu

last: Takeda

state: Osaka

address: 2-2-E2 Yamadaoka

department: Gastroenterological Surgery

institute: Osaka University Graduate School of Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression v3 8x60K Microarray (Agilent, G4851C) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. The 75th percentile shift normalization and baseline transformation (baseline to median of all samples) were performed using Agilent GeneSpring GX.

source_name: colon cancer PDX model, Case2, Control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the miRNeasy mini kit (QIAGEN) with the on-column DNase digestion according to the manufacturer's recommendations.

tag: host strain

value: NOD/SCID mice

tag: tumor type

value: colon cancer

tag: treatment

value: vehicle


title: Case2 MQ

source_name: colon cancer PDX model, Case2, MQ

value: mefloquine


title: Case2 ML

source_name: colon cancer PDX model, Case2, ML

value: mefloquine with trans-l-diaminocyclohexane oxalatoplatinum


title: Case2 CQ

source_name: colon cancer PDX model, Case2, CQ

value: chloroquine


title: RRBS Glioblastoma patient pat_110 Surg.2 frozen [pat_110_N1917_12_fv]

value: wildtype

value: MedUni Vienna

value: Glioblastoma patient


title: RRBS Glioblastoma patient pat_110 Surg.1 frozen [pat_110_N1020_10_fv]

value: No

value: frozen


title: Case1 ML

source_name: colon cancer PDX model, Case1, ML


title: RRBS Glioblastoma patient pat_133 Surg.1 FFPE [pat_133_N268_09]


title: Case1 MQ

source_name: colon cancer PDX model, Case1, MQ


title: RRBS Low-grade glioma patient pat_108 Surg.5 frozen [pat_108_N54_13_fv]

value: Low-grade glioma patient


title: Case1 CQ

source_name: colon cancer PDX model, Case1, CQ


title: RRBS Glioblastoma patient pat_028 Surg.2 frozen [pat_028_N1164_14_fv]


title: WT_ESC_rep1

city: Shanghai

first: Zeyidan

last: Jiapaer

address: No.1239, Siping Road

institute: Tongji University

description: Gene expression of shCtrl mESCs

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: Embryonic stem cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer

growth_protocol: The mESC line 46C was cultured in 15% serum + LIF (1,000 U/ml, Millipore) on a feeder

extract_protocol: RNA was prepared using the RNAiso (Takara) following the manufacturer's recommendations.

treatment_protocol: mESCs were harvested after removing the feeder,and RNA was harvested using Trizol reagent

value: shCtrl


title: RRBS Glioblastoma patient pat_043 Surg.1 frozen [pat_043_N486_13_fv]


title: LincU_KD_ESC_rep1

description: Gene expression of lincU knockdown mESCs

value: shLincU


title: RRBS Glioblastoma patient pat_027 Surg.1 frozen [pat_027_N879_12_fv]


title: RRBS Low-grade glioma patient pat_108 Surg.6 frozen [pat_108_N1196_13_fv]


title: RRBS Glioblastoma patient pat_027 Surg.2 frozen [pat_027_N1154_13_fv]


title: RRBS Glioblastoma patient ind_43 Surg.NA frozen [ind_43_N656_15_fv]


title: RRBS Glioblastoma patient pat_021 Surg.2 frozen [pat_021_N838_13_fv]


title: RRBS Glioblastoma patient ind_32 Surg.NA frozen [ind_32_N1575_12_fv]


title: Control1

source_name: colon cancer PDX model, Case1, Control


title: mm_BMDM_PpargKO_1st_stim_3hIL4_RNA_rep2

city: South San Francisco

first: Bence

last: Daniel

address: 1 DNA Way

department: Department Proteomic and Genomic Technologies

institute: Genentech Inc.

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
memory_averaged.cpm.table.tsv
KO_ctrl_3h_IL4

data_processing:
Samples were aligned with TopHat v2.0.7 using default parameters.
CPM values were calculated by cufflinks v2.0.2 using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: table (tsv) of averaged CPM values

source_name: PPARgKO_ctrl_3h_IL4_RNA-seq analysis of PpargKO BMDMs treated with IL-4_2

growth_protocol: Cells were isolated from the bone marrow, then differentiated for 6 days in the presence of MCSF followed by the indicated treatments.

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

treatment_protocol: Cells were exposed to 20ng/ul IL-4 for 24 hours or left untreated followed by wash out and incubation in differentiation media for an additional 24 hours. Control cells and IL-4 pre-treated cells were stimulated with IL-4 for 3 hours and then collected in Trizol.

tag: strain

value: Bone marrow-derived macrophage

tag: age

value: 3 months

tag: Sex

value: male


title: mm_BMDM_PpargKO_1st_stim_3hIL4_RNA_rep1

source_name: PPARgKO_ctrl_3h_IL4_RNA-seq analysis of PpargKO BMDMs treated with IL-4_1


title: mm_BMDM_PpargKO_2nd_stim_3hIL4_RNA_rep2

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
memory_averaged.cpm.table.tsv
KO_IL4_pre_3h_IL4

source_name: PPARgKO_IL4_pre_3h_IL4_RNA-seq analysis of PpargKO BMDMs pre-treated with IL-4 for 24 hours followed by washout, incubation for an additional 24 hours in regular differentiation media and then restimulated with IL-4 _2


title: mm_BMDM_PpargKO_2nd_stim_ctrl_RNA_rep2

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
memory_averaged.cpm.table.tsv
KO_IL4_pre_0h

source_name: PPARgKO_IL4_pre_0h_RNA-seq analysis of PpargKO BMDMs pre-treated with IL-4 for 24 hours followed by washout, incubation for an additional 24 hours in regular differentiation media_2


title: mm_BMDM_PpargKO_2nd_stim_ctrl_RNA_rep1

source_name: PPARgKO_IL4_pre_0h_RNA-seq analysis of PpargKO BMDMs pre-treated with IL-4 for 24 hours followed by washout, incubation for an additional 24 hours in regular differentiation media_1


title: mm_BMDM_PpargKO_2nd_stim_3hIL4_RNA_rep1

source_name: PPARgKO_IL4_pre_3h_IL4_RNA-seq analysis of PpargKO BMDMs pre-treated with IL-4 for 24 hours followed by washout, incubation for an additional 24 hours in regular differentiation media and then restimulated with IL-4 _1


title: mm_BMDM_PpargKO_1st_stim_ctrl_RNA_rep1

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
memory_averaged.cpm.table.tsv
KO_ctrl_0h

source_name: PPARgKO_ctrl_0h_RNA-seq analysis of PpargKO BMDMs_1


title: RRBS Glioblastoma patient ind_133 Surg.NA frozen [ind_133_N779_12_fv]

source_name: brain (tumor)

tag: idh status

tag: center

tag: sample group


title: mm_BMDM_PpargKO_1st_stim_ctrl_RNA_rep2

source_name: PPARgKO_ctrl_0h_RNA-seq analysis of PpargKO BMDMs_2


title: RRBS Glioblastoma patient pat_103 Surg.2 frozen [pat_103_N1934_14_fv]

tag: surgery number

tag: multisector

tag: sample type


title: mm_BMDM_Wt_2nd_stim_3hIL4_RNA_rep1

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
memory_averaged.cpm.table.tsv
WT_IL4_pre_3h_IL4

source_name: Wt_IL4_pre_3h_IL4_RNA-seq analysis of BMDMs pre-treated with IL-4 for 24 hours followed by washout, incubation for an additional 24 hours in regular differentiation media and then restimulated with IL-4 _1


title: mm_BMDM_Wt_2nd_stim_3hIL4_RNA_rep2

source_name: Wt_IL4_pre_3h_IL4_RNA-seq analysis of BMDMs pre-treated with IL-4 for 24 hours followed by washout, incubation for an additional 24 hours in regular differentiation media and then restimulated with IL-4 _2


title: RRBS Low-grade glioma patient pat_126 Surg.2 FFPE [pat_126_N_561_11]

value: mutant

value: FFPE


title: RRBS Low-grade glioma patient pat_127 Surg.1 FFPE [pat_127_N1101_03B]


title: RRBS Low-grade glioma patient pat_127 Surg.2 FFPE [pat_127_N781_12C]


title: RRBS Low-grade glioma patient pat_126 Surg.1 FFPE [pat_126_N901_07_A]


title: RRBS Low-grade glioma patient pat_125 Surg.2 FFPE [pat_125_N_795_13]


title: RRBS Low-grade glioma patient pat_125 Surg.1 FFPE [pat_125_N282_08]


title: mm_BMDM_Wt_2nd_stim_ctrl_RNA_rep1

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
memory_averaged.cpm.table.tsv
WT_IL4_pre_0h

source_name: Wt_IL4_pre_0h_RNA-seq analysis of BMDMs pre-treated with IL-4 for 24 hours followed by washout, incubation for an additional 24 hours in regular differentiation media_1


title: mm_BMDM_Wt_2nd_stim_ctrl_RNA_rep2

source_name: Wt_IL4_pre_0h_RNA-seq analysis of BMDMs pre-treated with IL-4 for 24 hours followed by washout, incubation for an additional 24 hours in regular differentiation media_2


title: RRBS Low-grade glioma patient pat_124 Surg.3 FFPE [pat_124_N_778_11]


title: RRBS Low-grade glioma patient pat_123 Surg.3 FFPE [pat_123_N289_04A]


title: mm_BMDM_Wt_1st_stim_3hIL4_RNA_rep2

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
memory_averaged.cpm.table.tsv
WT_ctrl_3h_IL4

source_name: Wt_3h_IL4_RNA-seq analysis of BMDMs treated with IL-4_2


title: RRBS Low-grade glioma patient pat_122 Surg.3 FFPE [pat_122_N697_11A]


title: RRBS Low-grade glioma patient pat_122 Surg.2 FFPE [pat_122_N41_05A]


title: mm_BMDM_Wt_1st_stim_3hIL4_RNA_rep1

source_name: Wt_3h_IL4_RNA-seq analysis of BMDMs treated with IL-4_1


title: mm_BMDM_Wt_1st_stim_ctrl_RNA_rep2

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
memory_averaged.cpm.table.tsv
WT_ctrl_0h

source_name: Wt_ctrl_0h_RNA-seq analysis of BMDMs_2


title: RRBS Glioblastoma patient pat_121 Surg.2 FFPE [pat_121_N1995_15]


title: RRBS Glioblastoma patient pat_120 Surg.1 FFPE [pat_120_N1512_14B]


title: RRBS Glioblastoma patient pat_110 Surg.2 frozen [pat_110_N1916_12_f]


title: RRBS Low-grade glioma patient pat_122 Surg.1 FFPE [pat_122_N1137_98]


title: RRBS Glioblastoma patient pat_110 Surg.1 frozen [pat_110_N1020_10_f]


title: RRBS Glioblastoma patient pat_120 Surg.2 FFPE [pat_120_N444_16B_1]


title: RRBS Glioblastoma patient pat_119 Surg.2 FFPE [pat_119_N883_16A]


title: RRBS Low-grade glioma patient pat_108 Surg.3 FFPE [pat_108_N294_10_C]


title: mm_BMDM_24hIL4pGW9662_RNA_rep2

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
antagonist_averaged.cpm.table.tsv
IL4_GW9662_24h

source_name: IL4_GW9662_RNA-seq analysis of BMDMs treated with IL-4+GW9662 for 24 hours_2


title: RRBS Glioblastoma patient pat_121 Surg.1 FFPE [pat_121_N2613_14C]


title: RRBS Glioblastoma patient pat_119 Surg.1 FFPE [pat_119_N200_15]


title: RRBS Glioblastoma patient pat_118 Surg.1 FFPE [pat_118_N2566_15_B]


title: RRBS Low-grade glioma patient pat_124 Surg.2 FFPE [pat_124_N_541_09]


title: RRBS Low-grade glioma patient pat_108 Surg.2 FFPE [pat_108_N1764_06]


title: mm_BMDM_24hIL4pGW9662_RNA_rep1

source_name: IL4_GW9662_RNA-seq analysis of BMDMs treated with IL-4+GW9662 for 24 hours_1


title: RRBS Low-grade glioma patient pat_107 Surg.2 FFPE [pat_107_N234_09_C]


title: RRBS Glioblastoma patient pat_117 Surg.2 FFPE [pat_117_N269_16]


title: RRBS Glioblastoma patient pat_117 Surg.1 FFPE [pat_117_N759_15B]


title: RRBS Low-grade glioma patient pat_123 Surg.4 FFPE [pat_123_N1453_06B]


title: RRBS Glioblastoma patient pat_118 Surg.2 FFPE [pat_118_N2515_15C]


title: RRBS Glioblastoma patient pat_116 Surg.2 FFPE [pat_116_Graz_12_3_2011]

value: Graz


title: mm_BMDM_24hIL4pVeh_RNA_rep2

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
antagonist_averaged.cpm.table.tsv
IL4_24h

source_name: IL4_24h_RNA-seq analysis of BMDMs treated with IL-4+DMSO:EtOH for 24 hours_2


title: RRBS Low-grade glioma patient pat_107 Surg.3 FFPE [pat_107_N1330_09]


title: RRBS Glioblastoma patient pat_116 Surg.1 FFPE [pat_116_Graz_12_2_2011]


title: mm_BMDM_24hIL4pVeh_RNA_rep1

source_name: IL4_24h_RNA-seq analysis of BMDMs treated with IL-4+DMSO:EtOH for 24 hours_1


title: RRBS Glioblastoma patient pat_106 Surg.1 FFPE [pat_106_N995_11]

value: Salzburg


title: mm_BMDM_Wt_1st_stim_ctrl_RNA_rep1

source_name: Wt_ctrl_0h_RNA-seq analysis of BMDMs_1


title: RRBS Glioblastoma patient pat_114 Surg.2 FFPE [pat_114_Graz_10_3_2009]


title: RRBS Glioblastoma patient pat_114 Surg.1 FFPE [pat_114_Graz_10_1_2009]


title: RRBS Glioblastoma patient pat_106 Surg.2 FFPE [pat_106_N2264_13]


title: RRBS Glioblastoma patient pat_113 Surg.3 FFPE [pat_113_Graz_9_8_2014]


title: mm_BMDM_ctrl_24hGW9662_RNA_rep2

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
antagonist_averaged.cpm.table.tsv
GW9662_24h

source_name: GW9662_24h_RNA-seq analysis of BMDMs treated with GW9662 for 24 hours_2


title: RRBS Glioblastoma patient pat_113 Surg.2 FFPE [pat_113_Graz_9_4_2012]


title: mm_BMDM_ctrl_24hGW9662_RNA_rep1

source_name: GW9662_24h_RNA-seq analysis of BMDMs treated with GW9662 for 24 hours_1


title: RRBS Glioblastoma patient pat_113 Surg.1 FFPE [pat_113_Graz_9_2_2011]


title: RRBS Glioblastoma patient pat_112 Surg.2 FFPE [pat_112_Graz_5_4_2009]


title: RRBS Glioblastoma patient pat_104 Surg.2 FFPE [pat_104_N2462_15]


title: mm_BMDM_ctrl_24hVeh_RNA_rep2

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
antagonist_averaged.cpm.table.tsv
veh_24h

source_name: veh_24h_RNA-seq analysis of BMDMs treated with DMSO:EtOH for 24 hours_2


title: mm_BMDM_ctrl_24hVeh_RNA_rep1

source_name: veh_24h_RNA-seq analysis of BMDMs treated with DMSO:EtOH for 24 hours_1


title: RRBS Glioblastoma patient pat_103 Surg.3 FFPE [pat_103_N475_15]

source_name: brain (tumor)


title: RRBS Glioblastoma patient pat_111 Surg.1 FFPE [pat_111_Graz_4_1_2010]


title: RRBS Glioblastoma patient pat_111 Surg.2 FFPE [pat_111_Graz_4_5_2010]


title: RRBS Glioblastoma patient pat_103 Surg.1 FFPE [pat_103_N2083_13_A]


title: RRBS Glioblastoma patient pat_110 Surg.1 RCL [pat_110_N1020_10_rk]

value: RCL


title: RRBS Glioblastoma patient pat_102 Surg.2 FFPE [pat_102_N733_15_C]

value: Innsbruck


title: D4 DBA2J Ly6C low_Muscle isolated Ly6Clow macrophages at day 4 after CTX rep 1

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
D4 DBA2J Ly6C low

data_processing:
Samples were aligned with TopHat v2.0.7 using default parameters.
FPKM values were calculated by cufflinks v2.0.2 using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: table (csv) of FPKM values

source_name: Macrophages sorted from regenerating muscles after cadiotoxin induced injury of the Tibialis anterior muscle.

growth_protocol: Cells were sorted from regenerating muscles after cardiotoxin injury on the indicated days.

treatment_protocol: RNA was isolated with Trizol.

value: Tibialis anterior


title: D4 DBA2J Ly6C low_Muscle isolated Ly6Clow macrophages at day 4 after CTX rep 2


title: RRBS Low-grade glioma patient pat_108 Surg.4 FFPE [pat_108_N995_10]

value: MedUni Vienna


title: D4 DBA2J Ly6C low_Muscle isolated Ly6Clow macrophages at day 4 after CTX rep 3


title: RRBS Low-grade glioma patient pat_108 Surg.6 FFPE [pat_108_N1195_13_A]


title: RRBS Low-grade glioma patient pat_107 Surg.1 FFPE [pat_107_N840_01]


title: RRBS Glioblastoma patient pat_103 Surg.2 FFPE [pat_103_N1935_14]

value: wildtype

value: Glioblastoma patient


title: RRBS Glioblastoma patient pat_104 Surg.1 FFPE [pat_104_N2506_14_B]

value: No


title: RRBS Glioblastoma patient pat_112 Surg.1 FFPE [pat_112_Graz_5_1_2009]


title: RRBS Glioblastoma patient pat_097 Surg.2 FFPE [pat_097_N711_15]


title: RRBS Glioblastoma patient pat_101 Surg.2 FFPE [pat_101_N722_15]


title: D4 DBA2J Ly6C high_Muscle isolated Ly6Chigh macrophages at day 4 after CTX rep 2

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
D4 DBA2J Ly6C high


title: RRBS Glioblastoma patient pat_101 Surg.1 FFPE [pat_101_N721_15]


title: D4 DBA2J Ly6C high_Muscle isolated Ly6Chigh macrophages at day 4 after CTX rep 1


title: RRBS Glioblastoma patient pat_100 Surg.2 FFPE [pat_100_N720_15_B]


title: RRBS Glioblastoma patient pat_100 Surg.1 FFPE [pat_100_N719_15]


title: RRBS Low-grade glioma patient pat_108 Surg.1 FFPE [pat_108_N194_05_A]

value: Low-grade glioma patient


title: RRBS Low-grade glioma patient pat_108 Surg.5 FFPE [pat_108_N54_13]


title: D2 DBA2J Ly6C low_Muscle isolated Ly6Clow macrophages at day 2 after CTX rep 3

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
D2 DBA2J Ly6C low


title: D2 DBA2J Ly6C low_Muscle isolated Ly6Clow macrophages at day 2 after CTX rep 2


title: RRBS Glioblastoma patient pat_072 Surg.2 FFPE [pat_072_N2368_15I]

value: Yes


title: RRBS Glioblastoma patient pat_072 Surg.1 FFPE [pat_072_N2367_15I]


title: RRBS Glioblastoma patient pat_072 Surg.1 FFPE [pat_072_N2367_15II]


title: RRBS Glioblastoma patient pat_072 Surg.2 FFPE [pat_072_N2368_15_II]


title: RRBS Glioblastoma patient pat_072 Surg.2 FFPE [pat_072_N2368_15_III]


title: RRBS Glioblastoma patient pat_099 Surg.2 FFPE [pat_099_N715_15]


title: D2 DBA2J Ly6C low_Muscle isolated Ly6Clow macrophages at day 2 after CTX rep 1


title: RRBS Glioblastoma patient pat_057 Surg.3 FFPE [pat_057_N1190_15]

value: Linz


title: D4 DBA2J Ly6C high_Muscle isolated Ly6Chigh macrophages at day 4 after CTX rep 3


title: RRBS Glioblastoma patient pat_057 Surg.1 FFPE [pat_057_N1188_15]


title: RRBS Glioblastoma patient pat_057 Surg.2 FFPE [pat_057_N1189_15A]


title: RRBS Glioblastoma patient pat_102 Surg.1 FFPE [pat_102_N115_14]


title: RRBS Glioblastoma patient pat_072 Surg.1 FFPE [pat_072_N2367_15III]


title: D2 DBA2J Ly6C high_Muscle isolated Ly6Chigh macrophages at day 2 after CTX rep 3

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
D2 DBA2J Ly6C high


title: RRBS Glioblastoma patient pat_056 Surg.2 FFPE [pat_056_N1187_15]


title: RRBS Glioblastoma patient pat_098 Surg.2 FFPE [pat_098_N713_15]


title: RRBS Glioblastoma patient pat_056 Surg.1 FFPE [pat_056_N1186_15]


title: RRBS Glioblastoma patient pat_055 Surg.3 FFPE [pat_055_N1182_15]


title: RRBS Glioblastoma patient pat_055 Surg.2 FFPE [pat_055_N1181_15]


title: D2 DBA2J Ly6C high_Muscle isolated Ly6Chigh macrophages at day 2 after CTX rep 2


title: RRBS Glioblastoma patient pat_099 Surg.1 FFPE [pat_099_N714_15]


title: RRBS Glioblastoma patient pat_098 Surg.1 FFPE [pat_098_N712_15]


title: D2 DBA2J Ly6C high_Muscle isolated Ly6Chigh macrophages at day 2 after CTX rep 1


title: RRBS Glioblastoma patient pat_055 Surg.1 FFPE [pat_055_N1180_15]


title: RRBS Glioblastoma patient pat_054 Surg.2 FFPE [pat_054_N2488_14]

value: Klagenfurt


title: RRBS Glioblastoma patient pat_097 Surg.1 FFPE [pat_097_N710_15]


title: RRBS Glioblastoma patient pat_143 Surg.1 FFPE [pat_143_N1160_15]


title: RRBS Glioblastoma patient pat_054 Surg.1 FFPE [pat_054_N2487_14A]


title: D1 DBA2J Ly6C high_Muscle isolated Ly6Chigh macrophages at day 1 after CTX rep 3

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
D1 DBA2J Ly6C high

value: 3 months


title: RRBS Glioblastoma patient pat_050 Surg.1 FFPE [pat_050_N2456_14]


title: RRBS Glioblastoma patient pat_096 Surg.2 FFPE [pat_096_N707_15]


title: D1 DBA2J Ly6C high_Muscle isolated Ly6Chigh macrophages at day 1 after CTX rep 2

value: male


title: RRBS Glioblastoma patient pat_047 Surg.1 FFPE [pat_047_N2450_14]


title: RRBS Glioblastoma patient pat_049 Surg.1 FFPE [pat_049_N2454_14]


title: RRBS Glioblastoma patient pat_047 Surg.2 FFPE [pat_047_N2451_14]


title: RRBS Glioblastoma patient pat_093 Surg.2 FFPE [pat_093_N699_15]


title: D1 DBA2J Ly6C high_Muscle isolated Ly6Chigh macrophages at day 1 after CTX rep 1


title: D1 DBA2J Neu_Muscle isolated neutrophil at day 1 after CTX rep 1

description:
RNA was isolated with Trizol and approximately 2.5ug was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina). Poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.
D1 DBA2J Neu

source_name: Neutrophils sorted from regenerating muscles after cadiotoxin induced injury of the Tibialis anterior muscle.


title: RRBS Glioblastoma patient pat_053 Surg.2 FFPE [pat_053_N2482_14A]


title: RRBS Glioblastoma patient pat_051 Surg.2 FFPE [pat_051_N2461_14]


title: RRBS Glioblastoma patient pat_050 Surg.2 FFPE [pat_050_N2457_14]


title: RRBS Glioblastoma patient pat_094 Surg.2 FFPE [pat_094_N701_15_B]


title: RRBS Glioblastoma patient pat_051 Surg.1 FFPE [pat_051_N2460_14]


title: mm_BMDM_MCSFIL4_ATAC_rep1

data_processing:
alignment with bwa v0.7.10 using default parameters
bam generation with samtools v0.1.19 using default parameters
tag directory generation with homer v4.2 makeTagDirectory using -checkGC parameter
bedgraph generation with homer v4.2 makeUCSCfile using -fsize 1e50 -norm parameters
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF/IL4 (rep1)

extract_protocol:
Bone marrow-derived macrophages were differentiated in the presence of M-CSF for 6 days. Cells were treated with IL-4 (20ng/ul) for 24 hours. Cells were lysed in the following lysis buffer: 10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL.
Nuclei were resuspended in tagmentation reaction mixture (2ul TD enzyme, 25ul 2xTD buffer and 23ul H2O) and incubated for 30 minutes at 37C (Nextera DNA preparation kit: FC-121-1030, index kit: FC-121-1011). Reactions were stopped by the addition of EDTA and purified with Qiagen Minelute DNA preparation kit. Purified DNA was PCR amplified with KAPA PCR mix using 14 PCR cycles. PCR reactions were cleaned up with AMPure XP magnetic beads.

treatment_protocol: Cells were exposed to 20ng/ul IL-4 for 24 hours.

tag: method

value: ATAC-seq

tag: cell type

value: bone marrow-derived macrophage


title: RRBS Glioblastoma patient pat_095 Surg.2 FFPE [pat_095_N703_15]

value: FFPE


title: RRBS Glioblastoma patient pat_053 Surg.1 FFPE [pat_053_N2481_14]


title: RRBS Glioblastoma patient pat_052 Surg.1 FFPE [pat_052_N2477_14]


title: D1 DBA2J Neu_Muscle isolated neutrophil at day 1 after CTX rep 2


title: mm_BMDM_MCSFIL4_ATAC_rep2

source_name: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF/IL4 (rep2)


title: RRBS Glioblastoma patient pat_052 Surg.2 FFPE [pat_052_N2478_14]


title: RRBS Glioblastoma patient pat_045 Surg.2 FFPE [pat_045_N2447_14A]


title: mm_BMDM_MCSF_ATAC_rep2

source_name: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (rep2)


title: RRBS Glioblastoma patient pat_046 Surg.1 FFPE [pat_046_N2448_14]


title: RRBS Glioblastoma patient pat_093 Surg.1 FFPE [pat_093_N698_15]


title: RRBS Glioblastoma patient pat_096 Surg.1 FFPE [pat_096_N706_15]

value: mutant


title: RRBS Glioblastoma patient pat_095 Surg.1 FFPE [pat_095_N702_15]


title: RRBS Glioblastoma patient pat_094 Surg.1 FFPE [pat_094_N700_15_B]


title: RRBS Glioblastoma patient pat_046 Surg.2 FFPE [pat_046_N2449_14]


title: mm_BMDM_MCSF_ATAC_rep1

source_name: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (rep1)


title: RRBS Glioblastoma patient pat_045 Surg.1 FFPE [pat_045_N2446_14]


title: RRBS Glioblastoma patient pat_092 Surg.2 FFPE [pat_092_N695_15]


title: RRBS Glioblastoma patient pat_044 Surg.2 FFPE [pat_044_N820_07CI]


title: RRBS Glioblastoma patient pat_090 Surg.2 FFPE [pat_090_N688_15]


title: RRBS Glioblastoma patient pat_044 Surg.2 FFPE [pat_044_N820_07C]


title: mm_BMDM_Wt_24hIL4_ATAC

source_name: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4)


title: RRBS Glioblastoma patient pat_044 Surg.1 FFPE [pat_044_N669_06I]


title: RRBS Glioblastoma patient pat_044 Surg.1 FFPE [pat_044_N669_06III]


title: RRBS Glioblastoma patient pat_044 Surg.1 FFPE [pat_044_N669_06II]


title: RRBS Glioblastoma patient pat_092 Surg.1 FFPE [pat_092_N693_15]


title: mm_BMDM_PpargKO_24hIL4_ATAC

source_name: ATAC-Seq analysis of PpargKO mouse BMDM cells differentiated in the presence of MCSF (24hIL4)


title: RRBS Glioblastoma patient pat_090 Surg.1 FFPE [pat_090_N687_15]


title: mm_iBMDM_wtPparg_IL4_ATAC_rep2

source_name: ATAC-Seq analysis of PpargKO immortalized BMDMs transduced with wild type PPARg expressing lentivirus under the control of a doxycycline inducible promoter.


title: RRBS Glioblastoma patient pat_042 Surg.2 RCL [pat_042_N417_14_rk]

value: RCL


title: RRBS Glioblastoma patient pat_091 Surg.1 FFPE [pat_091_N689_15]

value: Innsbruck


title: RRBS Glioblastoma patient pat_091 Surg.2 FFPE [pat_091_N690_15]


title: RRBS Glioblastoma patient pat_043 Surg.1 FFPE [pat_043_N490_13B]


title: RRBS Glioblastoma patient pat_043 Surg.2 RCL [pat_043_N656_15_rk]


title: RRBS Glioblastoma patient pat_042 Surg.1 RCL [pat_042_N721_13_rk]


title: mm_BMDM_Wt_ctrl_ATAC

source_name: ATAC-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF


title: RRBS Glioblastoma patient pat_042 Surg.2 FFPE [pat_042_N417_14]


title: RRBS Glioblastoma patient pat_089 Surg.1 FFPE [pat_089_N686_15]


title: RRBS Glioblastoma patient pat_041 Surg.1 FFPE [pat_041_N623_04]

value: Rudolfstiftung


title: mm_iBMDM_wtPparg_IL4_ATAC_rep1


title: RRBS Glioblastoma patient pat_041 Surg.2 FFPE [pat_041_N1388_04]


title: RRBS Glioblastoma patient pat_044 Surg.2 FFPE [pat_044_N820_07CIII]

value: MedUni Vienna


title: RRBS Glioblastoma patient pat_044 Surg.2 FFPE [pat_044_N820_07CII]

value: wildtype


title: mm_BMDM_PpargKO_ctrl_ATAC

source_name: ATAC-Seq analysis of PpargKO mouse BMDM cells differentiated in the presence of MCSF


title: RRBS Glioblastoma patient pat_040 Surg.2 FFPE [pat_040_N174_14v]

value: Glioblastoma patient


title: RRBS Glioblastoma patient pat_089 Surg.2 FFPE [pat_089_N1283_13_B]

value: No


title: mm_iBMDM_wtPparg_ctrl_ATAC_rep2


title: mm_iBMDM_wtPparg_ctrl_ATAC_rep1


title: RRBS Glioblastoma patient pat_040 Surg.1 FFPE [pat_040_N1510_11]


title: RRBS Glioblastoma patient pat_038 Surg.1 FFPE [pat_038_N969_08]


title: RRBS Glioblastoma patient pat_038 Surg.2 RCL [pat_038_N225_09_rk]


title: RRBS Glioblastoma patient pat_040 Surg.2 RCL [pat_040_N173_14_rk]


title: RRBS Glioblastoma patient pat_087 Surg.2 FFPE [pat_087_N683_15]


title: RRBS Glioblastoma patient pat_037 Surg.1 FFPE [pat_037_N1059_07A]


title: RRBS Glioblastoma patient pat_088 Surg.2 FFPE [pat_088_N2310_13_D]


title: RRBS Glioblastoma patient pat_036 Surg.1 FFPE [pat_036_N986_07CIII]


title: mm_iBMDM_mutPparg_ctrl_ATAC_rep2

source_name: ATAC-Seq analysis of PpargKO immortalized BMDMs transduced with E499Q mutant PPARg expressing lentivirus under the control of a doxycycline inducible promoter..


title: mm_iBMDM_mutPparg_IL4_ATAC_rep1


title: RRBS Glioblastoma patient pat_049 Surg.2 FFPE [pat_049_N2455_14A]


title: RRBS Glioblastoma patient pat_037 Surg.2 FFPE [pat_037_N369_08]


title: RRBS Glioblastoma patient pat_086 Surg.1 FFPE [pat_086_N681_15]


title: mm_iBMDM_mutPparg_IL4_ATAC_rep2


title: RRBS Glioblastoma patient pat_036 Surg.1 FFPE [pat_036_N986_07A]


title: RRBS Glioblastoma patient pat_036 Surg.1 FFPE [pat_036_N986_07CII]


title: mm_iBMDM_Luc_IL4_ATAC_rep2

source_name: ATAC-Seq analysis of PpargKO immortalized BMDMs transduced with a luciferase expressing lentivirus.


title: RRBS Glioblastoma patient pat_036 Surg.2 FFPE [pat_036_N861_08AIII]


title: RRBS Glioblastoma patient pat_086 Surg.2 FFPE [pat_086_N605_13]


title: RRBS Glioblastoma patient pat_036 Surg.2 FFPE [pat_036_N861_08AII]


title: mm_iBMDM_Luc_IL4_ATAC_rep1


title: RRBS Glioblastoma patient pat_088 Surg.1 FFPE [pat_088_N684_15]


title: RRBS Glioblastoma patient pat_038 Surg.2 FFPE [pat_038_N225_09]


title: RRBS Glioblastoma patient pat_036 Surg.2 FFPE [pat_036_N861_08AI]


title: RRBS Glioblastoma patient pat_085 Surg.1 FFPE [pat_085_N359_14_B]


title: RRBS Glioblastoma patient pat_035 Surg.1 FFPE [pat_035_N1649_12]


title: mm_iBMDM_Luc_ctrl_ATAC_rep2


title: RRBS Glioblastoma patient pat_087 Surg.1 FFPE [pat_087_N1834_15]


title: mm_iBMDM_mutPparg_ctrl_ATAC_rep1


title: RRBS Glioblastoma patient pat_036 Surg.1 FFPE [pat_036_N986_07CI]


title: RRBS Glioblastoma patient pat_035 Surg.2 FFPE [pat_035_N1279_14A]


title: RRBS Glioblastoma patient pat_084 Surg.2 FFPE [pat_084_N762_14_B]


title: RRBS Glioblastoma patient pat_085 Surg.2 FFPE [pat_085_N1096_14_B]


title: RRBS Glioblastoma patient pat_084 Surg.1 FFPE [pat_084_N2298_13_D]


title: RRBS Glioblastoma patient pat_031 Surg.1 FFPE [pat_031_N441_06]


title: RRBS Glioblastoma patient pat_030 Surg.2 FFPE [pat_030_N918_15]


title: RRBS Glioblastoma patient pat_034 Surg.2 FFPE [pat_034_N158_07]

value: Salzburg


title: mm_BMDM_PpargKO_24hIL4_RAD21_rep2

source_name: RAD21 ChIP-Seq analysis of PpargKO mouse BMDM cells differentiated in the presence of MCSF followed by 24 hours of IL-4 exposure.

extract_protocol:
Bone marrow-derived macrophages were differentiated in the presence of M-CSF for 6 days. Cells were treated with IL-4 20ng/ul) for the indicated period of time and were double crosslinked and lysed. Immunoprecipitation was carried out with antibodies against PU.1 (sc-352), STAT6 (sc-981), RXR (sc-774), PPARγ (Perseus #PP-A3409A), P300 (sc-585), RNAPII-pS2 (ab5095) and RAD21 (ab992). Protein antibody complexes were washed six times and eluted from Protein A coated paramagnetic beads. DNA was purified with the Qiagen Minelute kit.
Libraries were prepared with the Ovation Ultralow Library Systems (Nugen) according to the manufacturer protocol.

treatment_protocol: Cells were exposed to 20ng/ul IL-4 and/or 1uM GW9662 with the appropriate volume of vehicle control (DMSO:EtOH).

tag: chip antibody


title: mm_iBMDM_Luc_ctrl_ATAC_rep1


title: RRBS Glioblastoma patient pat_033 Surg.1 FFPE [pat_033_N1161_06]


title: RRBS Glioblastoma patient pat_083 Surg.1 FFPE [pat_083_N679_15]


title: RRBS Glioblastoma patient pat_032 Surg.1 FFPE [pat_032_N1576_12]


title: RRBS Glioblastoma patient pat_030 Surg.1 FFPE [pat_030_N2441_14C]


title: mm_BMDM_PpargKO_24hIL4_RAD21_rep1


title: RRBS Glioblastoma patient pat_083 Surg.2 FFPE [pat_083_N1496_13_C]


title: mm_BMDM_PpargKO_ctrl_RAD21_rep2

source_name: RAD21 ChIP-Seq analysis of PpargKO mouse BMDM cells differentiated in the presence of MCSF.


title: RRBS Glioblastoma patient pat_029 Surg.2 FFPE [pat_029_N536_07]


title: RRBS Glioblastoma patient pat_028 Surg.1 FFPE [pat_028_N853_13A]


title: mm_BMDM_PpargKO_ctrl_RAD21_rep1


title: RRBS Glioblastoma patient pat_028 Surg.2 RCL [pat_028_N1165_14_rk]


title: RRBS Glioblastoma patient pat_082 Surg.1 FFPE [pat_082_N910_14_B]


title: RRBS Glioblastoma patient pat_027 Surg.1 RCL [pat_027_N886_12_rk]


title: RRBS Glioblastoma patient pat_028 Surg.2 FFPE [pat_028_N1165_14A]


title: RRBS Glioblastoma patient pat_082 Surg.2 FFPE [pat_082_N2041_14_D]


title: RRBS Glioblastoma patient pat_027 Surg.2 FFPE [pat_027_N1154_13]


title: RRBS Glioblastoma patient pat_027 Surg.1 FFPE [pat_027_N886_12]


title: RRBS Glioblastoma patient pat_081 Surg.2 FFPE [pat_081_N678_15]


title: mm_BMDM_Wt_24hIL4_RAD21_rep1

source_name: RAD21 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF followed by 24 hours of IL-4 exposure.


title: RRBS Glioblastoma patient pat_029 Surg.1 FFPE [pat_029_N127_05A]

source_name: brain (tumor)


title: mm_BMDM_Wt_ctrl_RAD21_rep2

source_name: RAD21 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF


title: RRBS Glioblastoma patient pat_026 Surg.1 FFPE [pat_026_N554_03B]


title: RRBS Glioblastoma patient pat_081 Surg.1 FFPE [pat_081_N677_15]


title: RRBS Glioblastoma patient pat_026 Surg.2 FFPE [pat_026_N1814_09A]


title: RRBS Glioblastoma patient pat_080 Surg.1 FFPE [pat_080_N2403_15]


title: RRBS Glioblastoma patient pat_080 Surg.2 FFPE [pat_080_N2189_15]


title: mm_BMDM_Wt_ctrl_RAD21_rep1


title: RRBS Glioblastoma patient pat_025 Surg.2 FFPE [pat_025_N259_08]


title: mm_BMDM_PpargKO_ctrl_P300_rep2

source_name: P300 ChIP-Seq analysis of PpargKO mouse BMDM cells differentiated in the presence of MCSF.


title: mm_BMDM_PpargKO_24hIL4_P300_rep1

source_name: P300 ChIP-Seq analysis of PpargKO mouse BMDM cells differentiated in the presence of MCSF followed by 24 hours of IL-4 exposure.


title: RRBS Glioblastoma patient pat_024 Surg.2 FFPE [pat_024_N1844_13B]


title: RRBS Glioblastoma patient pat_024 Surg.2 RCL [pat_024_N1844_13_rk]


title: RRBS Glioblastoma patient pat_024 Surg.1 FFPE [pat_024_N1132_12B]


title: RRBS Glioblastoma patient pat_023 Surg.2 FFPE [pat_023_N1735_09]


title: RRBS Glioblastoma patient pat_079 Surg.2 FFPE [pat_079_N2386_15]


title: RRBS Glioblastoma patient pat_023 Surg.1 FFPE [pat_023_N893_08]


title: RRBS Glioblastoma patient pat_079 Surg.1 FFPE [pat_079_N2385_15]


title: RRBS Glioblastoma patient pat_021 Surg.2 FFPE [pat_021_N845_13]


title: RRBS Glioblastoma patient pat_020 Surg.1 RCL [pat_020_N1180_10_rk]


title: mm_BMDM_PpargKO_ctrl_P300_rep1


title: RRBS Glioblastoma patient pat_020 Surg.2 RCL [pat_020_N1317_12_rk]


title: RRBS Glioblastoma patient pat_026 Surg.2 RCL [pat_026_N1814_09_rk]


title: RRBS Glioblastoma patient pat_019 Surg.2 FFPE [pat_019_N2490_14]


title: mm_BMDM_Wt_24hIL4_RAD21_rep2


title: RRBS Glioblastoma patient pat_019 Surg.1 FFPE [pat_019_N2489_14]


title: RRBS Glioblastoma patient pat_078 Surg.1 FFPE [pat_078_N2383_15]


title: mm_BMDM_PpargKO_24hIL4_P300_rep2


title: RRBS Glioblastoma patient pat_018 Surg.2 FFPE [pat_018_N1233_15]


title: RRBS Glioblastoma patient pat_018 Surg.3 FFPE [pat_018_N1234_15]


title: RRBS Glioblastoma patient pat_077 Surg.3 FFPE [pat_077_N2382_15]


title: RRBS Glioblastoma patient pat_018 Surg.1 FFPE [pat_018_N1232_15]


title: mm_BMDM_Wt_ctrl_P300_rep2

source_name: P300 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF


title: RRBS Glioblastoma patient pat_017 Surg.3 FFPE [pat_017_N1225_15A]


title: RRBS Glioblastoma patient pat_077 Surg.2 FFPE [pat_077_N2381_15]


title: RRBS Glioblastoma patient pat_017 Surg.2 FFPE [pat_017_N1224_15B]


title: mm_BMDM_Wt_ctrl_P300_rep1


title: RRBS Glioblastoma patient pat_017 Surg.1 FFPE [pat_017_N1223_15]


title: RRBS Glioblastoma patient pat_016 Surg.1 FFPE [pat_016_N960_03]


title: mm_BMDM_24hIL4_GW9662_P300_rep2

source_name: P300 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF followed by 24 hours of IL-4/GW9662 exposure.


title: RRBS Glioblastoma patient pat_016 Surg.2 FFPE [pat_016_N1248_04]


title: RRBS Glioblastoma patient pat_016 Surg.3 FFPE [pat_016_N465_05C]


title: RRBS Glioblastoma patient pat_076 Surg.2 FFPE [pat_076_N2378_15]


title: mm_BMDM_24hIL4_GW9662_P300_rep1


title: mm_BMDM_Wt_24hIL4_P300_rep1

source_name: P300 ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF followed by 24 hours of IL-4 exposure.


title: RRBS Glioblastoma patient pat_078 Surg.2 FFPE [pat_078_N2384_15]


title: RRBS Glioblastoma patient pat_015 Surg.3 FFPE [pat_015_N386_06]


title: mm_BMDM_Wt_24hIL4_P300_rep2


title: RRBS Glioblastoma patient pat_076 Surg.1 FFPE [pat_076_N1315_11_B]


title: mm_BMDM_24hIL4_veh_P300_rep2


title: RRBS Glioblastoma patient pat_075 Surg.2 FFPE [pat_075_N2377_15]


title: RRBS Glioblastoma patient pat_015 Surg.2 FFPE [pat_015_N1106_05]


title: mm_BMDM_24hIL4_veh_P300_rep1


title: RRBS Glioblastoma patient pat_014 Surg.2 FFPE [pat_014_N2463_14]


title: RRBS Glioblastoma patient pat_075 Surg.1 FFPE [pat_075_N2376_15]


title: RRBS Glioblastoma patient pat_014 Surg.4 FFPE [pat_014_N2465_14A]


title: mm_BMDM_ctrl_P300_rep2


title: RRBS Glioblastoma patient pat_074 Surg.3 FFPE [pat_074_N2375_15]


title: RRBS Glioblastoma patient pat_014 Surg.1 FFPE [pat_014_N2462_14]


title: mm_BMDM_ctrl_P300_rep1


title: RRBS Glioblastoma patient pat_012 Surg.3 FFPE [pat_012_N1220_15_III]

value: Yes


title: RRBS Glioblastoma patient pat_013 Surg.2 FFPE [pat_013_N1238_15]


title: RRBS Glioblastoma patient pat_077 Surg.1 FFPE [pat_077_N2380_15_C]


title: RRBS Glioblastoma patient pat_074 Surg.2 FFPE [pat_074_N2374_15]


title: mm_BMDM_24hIL4_GW9662_PPARg_rep2

source_name: PPARg ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF followed by 24 hours of IL-4/GW9662 exposure.

value: PPARg (Perseus #PP-A3409A)


title: RRBS Glioblastoma patient pat_012 Surg.3 FFPE [pat_012_N1220_15_II]

value: Linz


title: RRBS Glioblastoma patient pat_012 Surg.3 FFPE [pat_012_N1220_15]


title: RRBS Glioblastoma patient pat_012 Surg.2 FFPE [pat_012_N1219_15_II]


title: RRBS Glioblastoma patient pat_074 Surg.1 FFPE [pat_074_N2373_15]


title: mm_BMDM_24hIL4_GW9662_PPARg_rep1

value: 3 months


title: RRBS Glioblastoma patient pat_073 Surg.2 FFPE [pat_073_N2372_15]


title: RRBS Glioblastoma patient pat_012 Surg.2 FFPE [pat_012_N1219_15]


title: RRBS Glioblastoma patient pat_012 Surg.1 FFPE [pat_012_N1218_15_I]


title: RRBS Glioblastoma patient pat_073 Surg.1 FFPE [pat_073_N2371_15_B]


title: RRBS Glioblastoma patient pat_012 Surg.1 FFPE [pat_012_N1218_15]


title: RRBS Glioblastoma patient pat_015 Surg.1 FFPE [pat_015_N139_03C]


title: mm_BMDM_24hIL4_veh_PPARg_rep2

source_name: PPARg ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF followed by 24 hours of IL-4 exposure.

value: male


title: RRBS Glioblastoma patient pat_072 Surg.2 FFPE [pat_072_N2368_15]


title: RRBS Glioblastoma patient pat_011 Surg.3 FFPE [pat_011_N1201_15]


title: mm_BMDM_24hIL4_veh_PPARg_rep1


title: mm_BMDM_ctrl_PPARg_rep2

source_name: PPARg ChIP-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF.


title: RRBS Glioblastoma patient pat_013 Surg.1 FFPE [pat_013_N1237_15]


title: RRBS Glioblastoma patient pat_072 Surg.1 FFPE [pat_072_N2367_15]


title: mm_BMDM_ctrl_PPARg_rep1


title: RRBS Glioblastoma patient pat_071 Surg.2 FFPE [pat_071_N2363_15_C]


title: mm_BMDM_24hIL4_GW9662_PolIIpS2_rep2

source_name: RNAPII-pS2 ChIP-seq analysis of mouse bone marrow-derived macrophages differentiated in the presence of MCSF and treated with IL-4 for 24 hours followed by GW9662 exposure for 1 hour.

value: PolII-pS2 (ab5095)


title: RRBS Glioblastoma patient pat_071 Surg.1 FFPE [pat_071_N2362_15]


title: mm_BMDM_24hIL4_GW9662_PolIIpS2_rep1

value: bone marrow-derived macrophage


title: RRBS Glioblastoma patient pat_070 Surg.2 FFPE [pat_070_N1247_15]

value: FFPE


title: RRBS Glioblastoma patient pat_070 Surg.1 FFPE [pat_070_N1246_15]


title: RRBS Glioblastoma patient pat_069 Surg.2 FFPE [pat_069_N1245_15]


title: RRBS Glioblastoma patient pat_068 Surg.2 FFPE [pat_068_N1242_15_A]


title: RRBS Glioblastoma patient pat_069 Surg.1 FFPE [pat_069_N1243_15]


title: RRBS Glioblastoma patient pat_007 Surg.1 FFPE [pat_007_N1197_15]


title: RRBS Glioblastoma patient pat_006 Surg.2 FFPE [pat_006_N1231_15]


title: RRBS Glioblastoma patient pat_006 Surg.1 FFPE [pat_006_N1230_15]


title: RRBS Glioblastoma patient pat_008 Surg.1 FFPE [pat_008_N1250_15_II]


title: RRBS Glioblastoma patient pat_011 Surg.1 FFPE [pat_011_N1199_15B]


title: RRBS Glioblastoma patient pat_008 Surg.2 FFPE [pat_008_N1252_15A_II]


title: RRBS Glioblastoma patient pat_010 Surg.3 FFPE [pat_010_N1222_15]


title: RRBS Glioblastoma patient pat_011 Surg.2 FFPE [pat_011_N1200_15]


title: RRBS Glioblastoma patient pat_010 Surg.1 FFPE [pat_010_N1436_06]


title: RRBS Glioblastoma patient pat_011 Surg.1 FFPE [pat_011_N1199_15B_I]


title: RRBS Glioblastoma patient pat_011 Surg.2 FFPE [pat_011_N1200_15_I]


title: RRBS Glioblastoma patient pat_010 Surg.2 FFPE [pat_010_N1221_15]


title: RRBS Glioblastoma patient pat_009 Surg.2 FFPE [pat_009_N709_15]


title: RRBS Glioblastoma patient pat_008 Surg.1 FFPE [pat_008_N1250_15_I]


title: RRBS Glioblastoma patient pat_008 Surg.1 FFPE [pat_008_N1250_15]


title: RRBS Glioblastoma patient pat_008 Surg.2 FFPE [pat_008_N1252_15A_III]


title: RRBS Glioblastoma patient pat_068 Surg.1 FFPE [pat_068_N1241_15]


title: RRBS Glioblastoma patient pat_007 Surg.2 FFPE [pat_007_N1198_15]


title: RRBS Glioblastoma patient pat_005 Surg.2 FFPE [pat_005_N1203_15]


title: RRBS Glioblastoma patient pat_067 Surg.2 FFPE [pat_067_N1236_15]


title: RRBS Glioblastoma patient pat_009 Surg.1 FFPE [pat_009_N708_15]


title: RRBS Glioblastoma patient pat_008 Surg.2 FFPE [pat_008_N1252_15A]


title: RRBS Glioblastoma patient pat_067 Surg.1 FFPE [pat_067_N1235_15_A]


title: RRBS Glioblastoma patient pat_004 Surg.1 FFPE [pat_004_N1_08]


title: RRBS Glioblastoma patient pat_004 Surg.2 RCL [pat_004_N1420_08_rk]


title: RRBS Glioblastoma patient pat_004 Surg.2 FFPE [pat_004_N1420_08]


title: RRBS Glioblastoma patient pat_003 Surg.2 FFPE [pat_003_N1734_10]


title: RRBS Glioblastoma patient pat_066 Surg.2 FFPE [pat_066_N1229_15_A]


title: RRBS Glioblastoma patient pat_003 Surg.1 RCL [pat_003_N1109_10_rk]


title: RRBS Glioblastoma patient pat_064 Surg.2 FFPE [pat_064_N1213_15]


title: RRBS Glioblastoma patient pat_064 Surg.1 FFPE [pat_064_N1212_15]


title: RRBS Glioblastoma patient pat_063 Surg.1 FFPE [pat_063_N1210_15_B]


title: RRBS Glioblastoma patient pat_065 Surg.1 FFPE [pat_065_N1226_15]


title: RRBS Glioblastoma patient pat_063 Surg.2 FFPE [pat_063_M1211_15]


title: RRBS Glioblastoma patient pat_065 Surg.2 FFPE [pat_065_N1227_15]


title: RRBS Normal white matter control ind_114 Surg.N/A FFPE [ind_114_N321_15C]

source_name: brain (white matter)

value: Normal white matter control


title: RRBS Glioblastoma patient pat_066 Surg.1 FFPE [pat_066_N1228_15]


title: RRBS Glioblastoma patient pat_062 Surg.2 FFPE [pat_062_N1209_15]


title: RRBS Glioblastoma patient pat_005 Surg.1 FFPE [pat_005_N1202_15]


title: RRBS Normal white matter control ind_112 Surg.N/A FFPE [ind_112_N1471_11A]


title: RRBS Normal white matter control ind_113 Surg.N/A FFPE [ind_113_N61_15D]


title: RRBS Glioblastoma patient pat_002 Surg.2 RCL [pat_002_N1025_10_rk]

value: RCL


title: RRBS Normal white matter control ind_115 Surg.N/A FFPE [ind_115_N912_12F]


title: RRBS Glioblastoma patient pat_001 Surg.2 FFPE [pat_001_N1677_06]


title: RRBS Glioblastoma patient pat_002 Surg.2 FFPE [pat_002_N1025_10]


title: RRBS Glioblastoma patient pat_002 Surg.1 FFPE [pat_002_N380_09B]


title: RRBS Glioblastoma patient pat_003 Surg.1 FFPE [pat_003_N1109_10]


title: RRBS Normal white matter control ind_116 Surg.N/A FFPE [ind_116_N1783_14]


title: RRBS Glioblastoma patient pat_061 Surg.2 FFPE [pat_061_N1207_15]


title: RRBS Glioblastoma patient pat_060 Surg.2 FFPE [pat_060_N1205_15]


title: RRBS Glioblastoma patient pat_001 Surg.1 FFPE [pat_001_N1168_05A]


title: RRBS Glioblastoma patient pat_062 Surg.1 FFPE [pat_062_N1208_15_B]


title: RRBS Glioblastoma patient pat_060 Surg.1 FFPE [pat_060_N1204_15]


title: RRBS Glioblastoma patient pat_058 Surg.2 FFPE [pat_058_N1192_15]


title: RRBS Glioblastoma patient pat_059 Surg.2 FFPE [pat_059_N1196_15]


title: RRBS Glioblastoma patient pat_061 Surg.1 FFPE [pat_061_N1206_15]


title: RRBS Glioblastoma patient pat_058 Surg.1 FFPE [pat_058_N1191_15]


title: RRBS Glioblastoma patient pat_048 Surg.1 FFPE [pat_048_N2452_14]

value: Klagenfurt


title: RRBS Glioblastoma patient pat_048 Surg.2 FFPE [pat_048_N2453_14]


title: RRBS Glioblastoma patient pat_044 Surg.1 FFPE [pat_044_N668_06]


title: RRBS Glioblastoma patient pat_059 Surg.1 FFPE [pat_059_N1195_15]


title: RRBS Glioblastoma patient pat_043 Surg.2 FFPE [pat_043_N658_15D]


title: RRBS Glioblastoma patient pat_042 Surg.1 FFPE [pat_042_N721_13B]


title: RRBS Glioblastoma patient pat_042 Surg.2 frozen [pat_042_N417_14_f]

value: frozen


title: RRBS Glioblastoma patient pat_042 Surg.1 frozen [pat_042_N721_13_f]

value: MedUni Vienna