title: WT mice transplanted with WT bone marrow 1

description:
wild type transplanted with wild type bone marrow after 3 days under the hypoxia
Lung5


title: WT mice transplanted with triply n/i/eNOS-/- bone marrow 4

status: Public on Nov 03 2017

type: SRA

city: Kitakyushu

first: Takaaki

last: Ogoshi

state: Fukuoka

address: 1-1 Iseigaoka, Yahatanishi-ku

department: Department of Respiratory Medicine

country: Japan

institute: University of Occupational and Environmental Health,  Japan

description:
wild type transplanted with triply n/i/eNOS-/- bone marrow after 3 days under the hypoxia
Lung4

library_source: transcriptomic

data_processing:
CASAVA software (v1.8.2, Illumina, San Diego, CA) was used for basecalling.
The trimmed reads were mapped onto the reference mouse genome mm10 using TopHat program (v2.0.13) in combination with Bowtie2 (v2.2.3) and SAMtools (v0.1.19).
Gene expression was quantified with the Cufflinks program (v2.2.1).  We detected raw mapped reads and the fragments per kilobase of exon per million mapped fragments (FPKM)
Genome_build: mm10
Supplementary_files_format_and_content: Files containing normalized abundance measurements and raw counts of sequencing reads

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
Total RNA concentrations were determined by a spectrophotometer (NanoDrop 2000, Thermo Scientific, Wilmington, DE), and the quality of the total RNA samples was assessed by an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).  RNA integrity number (RIN) was ranging from 7.8 to 8.2 in the 8 samples.  mRNA was extracted using a Dynabeads mRNA Purfication Kit (Thermo,Waltham, MA), and cDNA was generated from 500 ng of mRNA using a PrimeScript Double Strand cDNA Synthesis Kit (Takara Bio, Otsu, Japan).  Fifty ng of each cDNA sample was sheared in 200-500 bp using the Covaris S220 (Covaris, Woburn, MA) and 75 bp single-end reads were prepared using KAPA Library Preparation Kits (Kapa Biosystems, Wilmington, MA).  The cDNA libraries were indexed for multiplexing, and were sequenced on the Illumina HiSeq 2500 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: Lung


title: OSDN001M_BC4

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

data_processing:
Color-space base calling
Mapping, alignment with Lifescope
Lifescope transcriptome workflow
Genome_build: hg19
Supplementary_files_format_and_content: counts data

organism: Homo sapiens

source_name: bone

growth_protocol: samples from the bone

extract_protocol:
Bone samples (40-50 mg) were grinded with nitrogen by pestle and mortar into powder and pretreated with trizol. Total RNA was extracted with RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia CA, USA) according to the manufacturer’s protocol.
50 ng of total RNA was amplified by applying Ovation RNA-Seq System V2 (NuGen, Emeryville, CA, USA) after which the resulting cDNAs were pooled in equal amount and the pool was used to prepare the DNA fragment library with SOLiD System chemistry (Life Technologies Corp., Carlsbad, CA, USA). Sequencing was performed using SOLiD 5500W platform and DNA sequencing chemistry (Life Technologies Corp., Carlsbad, CA, USA). Raw reads (75 bp) were color-space mapped to the human genome hg19 reference using Maxmapper algorithm implemented in the Lifescope software (Life Technologies, Ltd). Mapping to multiple locations was permitted. The quality threshold was set to 10 giving the mapping confidence more than 90. Reads with score less than 10 were filtered out. Average mapping quality was 30. Analysis of the RNA content and gene-based annotation was done within whole transcriptome workflow implemented in Lifescope.

treatment_protocol: opaired tumor and normal bone samples

tag: tumor

value: TUMOR

tag: Sex

value: male

tag: barcode


title: WT mice transplanted with WT bone marrow 4

description:
wild type transplanted with wild type bone marrow after 3 days under the hypoxia
Lung8


title: WT mice transplanted with WT bone marrow 3

description:
wild type transplanted with wild type bone marrow after 3 days under the hypoxia
Lung7


title: OSDN001B_BC3

value: NORMAL


title: WT mice transplanted with triply n/i/eNOS-/- bone marrow 1

description:
wild type transplanted with triply n/i/eNOS-/- bone marrow after 3 days under the hypoxia
Lung1


title: OSVN005M_BC9


title: WT mice transplanted with triply n/i/eNOS-/- bone marrow 2

description:
wild type transplanted with triply n/i/eNOS-/- bone marrow after 3 days under the hypoxia
Lung2


title: WT mice transplanted with triply n/i/eNOS-/- bone marrow 3

description:
wild type transplanted with triply n/i/eNOS-/- bone marrow after 3 days under the hypoxia
Lung3


title: OSVN001B_BC1

value: female


title: BC3_JQ1+PEP005

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

country: USA

institute: UC Davis School of Medicine

description: Illimuna next-generation sequencing (1x50bp, single read)

data_processing:
Image processing, base calling, quality scoring (Phred), FASTQ file generation, and sample demultiplexing were executed by HiSeq Control Software (v3.3.76) with Real Time Analysis (RTA2) software (Illumina; San Diego, CA).
The FASTQ-formatted sequence data was analyzed using a standard HISAT-Cufflinks workflow. In brief, raw sequence reads (FASTQ format) were aligned to the reference human genome assembly (Dec. 2013, GRCh38) using HISAT (hierarchical indexing for spliced alignment of transcripts) software. Gene- and transcript-level expression were comprehensively quantified with Cufflinks software, which performed 1) transcript assembly, 2) identification of splice variants, 3) quantification of expression as FPKM (fragments per kilobase of transcript per million mapped reads) values, and 4) normalization. Normalized FPKM values (Cuffnorm output) were utilized for downstream analysis steps.
Processed data are Cufflinks-Cuffnorm output files and contain Gene_Symbol (Ensembl ID), FPKM values, and FPKM status.
Genome_build: GRCh38, Dec. 2013
Supplementary_files_format_and_content: Tab-delimited text files include Gene_Symbol (Ensembl ID), FPKM values, and FPKM status for each transcript and were prepared from the Cufflinks-Cuffnorm gene-level output files.

source_name: BC3 cells cultured in medium with PEP005+JQ1.

growth_protocol: BC3 and HBL-6 cells were cultured in RPMI 1640 supplemented with 10% FBS. The BCBL-1 cell line was cultured in RPMI 1640 supplemented with 15% FBS. MCF-7 cells (ATCC HTB-22) were cultured in complete medium (DMEM, 10% FBS, Pen-Strep). The cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2 (v/v).

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen) from MCF-7 parental and TMR cells treated with or without 4-hydroxytamoxifen for 24 hours.
Indexed RNA-Seq libraries were prepared from 200 ng total RNA using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Inc.) according to the manufacturer’s protocol. Poly-adenylated mRNA was purified by binding to oligo(dT) beads and to remove rRNA, which was followed by fragmentation by incubation at 94ºC in the presence of magnesium. Double-stranded cDNA was then generated by random-primed first-strand synthesis and second strand synthesis in the presence of dUTP for strand marking. Subsequently, the cDNA was 3’-A tailed and indexed, Illumina-compatible adapters were ligated. The libraries were then enriched by high-fidelity PCR amplification (13 cycles) with KAPA HiFi HotStart DNA Polymerase and adapter-specific primers.

treatment_protocol: Each PEL cell line was seeded into at least 4 individual 25-cm^2 tissue culture flasks. After 2-3 days of grwth, the cells were treated with vehicle control (DMSO), JQ1, PEP005, or the combination (JQ1 + PEP005) for 24 hours.

tag: cell line

value: human primary effusion lymphoma


title: Gst_ex_1

city: Leipzig

first: Felix

middle: Georg Maria

last: Ernst

address: Bruederstrasse 34

department: Faculty of Bioscience

country: Germany

institute: University of Leipzig

description: tRNA

data_processing:
Genomes of Pha, Esi, Gst, and Bsu were scanned for tRNAs using tRNAscan-SE 1.3.1.
Sequenced reads were trimmed for adaptor sequences using cutadapt 1.11 and mapped to the corresponding set of genomic tRNAs counting all mapped as well as the different 3’-ends of the transcripts.
Genome_build: Bsu (NC_000964.3), Esi (NC_010556.1), Gst (NZ_CM002692.1), and Pha (NZ_CP016537.2)
Supplementary_files_format_and_content: Data files contain tRNA gene annotations and corresponding total read counts as well as read counts for different 3’-ends of tRNA transcripts.

organism: Geobacillus stearothermophilus

source_name: DSMZ 22

growth_protocol:
growth temperature: 55°C
For a preculture cells were grown in media suggested by DSMZ at the optimal temperature over night. Main cultures were inoculated at OD600 = 0.2 and grown to mid log phase. Half of the culture was harvested as the sample for exponential growth and the other half cultured over night until 24h of incubation time was reached. The remaining culture was harvested as the stationary samples. Each culture was run in triplicates.

extract_protocol:
Immediately after harvesting cells were treated with TriZOL to isolated total RNA as recommended by the manufacturer. Cell disruption was fascilitated by using FastPrep24 (6 m/s, 30 sec). To precipiated larger RNA species, samples were subjected to high salt precipitation using 5 M LiCl and the supernatant was desalted via G-25 spin filtration (PD-10; GE). RNA was ethanol precipitated and subjected to RiboZero treatment (Samples 3, 6, 9, 12, 15, 18, 23) or processed without further treatment.
A 3'-blocked oligonucleotide was adenylated (NEB #E2610) and ligated to the isolated RNA with a truncated T4-RNA-Ligase 2 (NEB #M0242). Ligation products were reverse transcribed (RevertAid; Thermo Scientific) using a 32P 5'-labeled primer and resulting cDNA was isolated from 10% denaturing gel. A pre-adenylated 3'-blocked oligonucleotide was ligated to isolated cDNA using a 5’-App-DNA/RNA-Ligase (NEB #M0319) at conditions given for ssDNA ligation. Ligation products were amplified by PCR in a 100 µL reaction for 15-16 cycles and isolated from MethylBlue stained gel. For each sample a indexed was introduced during PCR and one lane on MiSeq was used per replicate. The third sample from B. subtilis from stationary phase yielded a not sufficient DNA amount and did not generate usable sequence results.

treatment_protocol: cells were harvested by centrifugation at 2800 x g and processes further directly.


title: Gst_ex_2

description: tRNA


title: BC3_JQ1

source_name: BC3 cells cultured in medium with JQ1.


title: Gst_sta_1

description: tRNA


title: Gst_sta_3

description: tRNA


title: BC3_PEP005

source_name: BC3 cells cultured in medium with PEP005.


title: OSVN001L_BC2


title: Esi_ex_3

description: tRNA

organism: Exiguobacterium artemiae

growth_protocol:
growth temperature: 20°C
For a preculture cells were grown in media suggested by DSMZ at the optimal temperature over night. Main cultures were inoculated at OD600 = 0.2 and grown to mid log phase. Half of the culture was harvested as the sample for exponential growth and the other half cultured over night until 24h of incubation time was reached. The remaining culture was harvested as the stationary samples. Each culture was run in triplicates.


title: BC3_DMSO

source_name: BC3 cells cultured in medium with vehicle control.


title: AD_c3418CT_200

description: Ion Torrent S5

source_name: skin

growth_protocol: samples from the skin

extract_protocol:
After local anesthesia and under standard aseptic conditions, 4 mm punch biopsies were taken. After subcutaneous fat tissue removal, the skin biopsies were directly snap frozen in liquid nitrogen. To further minimize potential RNA degradation by skin RNAses, biopsies were not stored at -80° C, but directly processed for RNA extraction. Skin biopsies were homogenized in TRIZOL (Ambion, Austin, TX) and thereafter centrifuged to eliminate contaminating fat prior extraction with chloroform. After precipitation using isopropanol at -20°C, RNA was washed twice with ethanol and then re-suspended in Tris-EDTA buffer (Ambion, Austin, TX). Then, samples were incubated at 57°C for 10 min and RNA concentration was determined by using a NanoDrop (Thermoscientific, Waltham, MA). RNA quality was assessed by using a Bioanalyzer chip assay (Agilent technologies, Santa Clara, CA). Samples were stored at -80°C until RNA sequencing.
50 ng of total RNA were amplified by applying Ovation RNA-Seq System V2 (NuGen, Emeryville, CA). The resulting cDNAs were pooled in equal amount and used to prepare the DNA fragment library with SOLiD System chemistry (Life Technologies Corp., Carlsbad, CA). Sequencing was performed using SOLiD 5500W platform and DNA sequencing chemistry (Life Technologies Corp., Carlsbad, CA). Raw reads (75 bp) were color-space mapped to the human genome hg19 reference using Maxmapper algorithm implemented in the Lifescope software (Life Technologies Corp., Carlsbad, CA). Mapping to multiple locations was permitted. Reads with score less than 10 were excluded. Average mapping quality was 30. Analysis of the RNA content and gene-based annotation was done with whole-transcriptome work- flow of Lifescope.

treatment_protocol: mutation or wild-type

tag: disease

value: atopic dermatitis (AD)

tag: mutation

value: FLG mutation


title: Esi_ex_2

description: tRNA


title: BCBL-1_PEP005

source_name: BCBL-1 cells cultured in medium with PEP005.


title: BCBL-1_JQ1+PEP005

source_name: BCBL-1 cells cultured in medium with PEP005+JQ1.


title: HBL-6_PEP005

source_name: HBL-6 cells cultured in medium with PEP005.


title: HBL-6_DMSO

source_name: HBL-6 cells cultured in medium with vehicle control.


title: BCBL-1_JQ1

source_name: BCBL-1 cells cultured in medium with JQ1.


title: Esi_sta_3

description: tRNA


title: IV_2282del42447x_190

description: Ion Torrent S5

value: ichthyosis vulgaris (IV)


title: BCBL-1_DMSO

source_name: BCBL-1 cells cultured in medium with vehicle control.


title: Gst_ex_3

description: tRNA


title: HBL-6_JQ1+PEP005

source_name: HBL-6 cells cultured in medium with PEP005+JQ1.


title: Esi_sta_2

description: tRNA


title: HBL-6_JQ1

source_name: HBL-6 cells cultured in medium with JQ1.


title: IV_2282del42282del4_131

description: Ion Torrent S5


title: Esi_sta_1

description: tRNA


title: AD_2282del4_194

description: Ion Torrent S5


title: Esi_ex_1

description: tRNA


title: AD_2282del4_187

description: Ion Torrent S5


title: Gst_sta_2

description: tRNA


title: Pha_ex_3

description: tRNA

organism: Planococcus halocryophilus


title: IV_r501x2282del4_117

description: Ion Torrent S5


title: Pha_ex_2

description: tRNA


title: Bsu_ex_3

description: tRNA

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: DSMZ 10

growth_protocol:
growth temperature: 37°C
For a preculture cells were grown in media suggested by DSMZ at the optimal temperature over night. Main cultures were inoculated at OD600 = 0.2 and grown to mid log phase. Half of the culture was harvested as the sample for exponential growth and the other half cultured over night until 24h of incubation time was reached. The remaining culture was harvested as the stationary samples. Each culture was run in triplicates.

value: subsp. Subtilis strain 168


title: Input DNA of replicate 1 (GFF-1)

city: Wageningen

first: Marian

last: Bemer

address: Droevendaalsesteeg 1

department: Molecular Biology

country: Netherlands

institute: Wageningen University

library_source: genomic

data_processing:
GAPipeline-1.4.0
Alignment: Sequence reads were obtained and mapped to the Arabidopsis thaliana genome using the SOAP mapping software (soap.genomics.org.cn/). All reads mapping with two or fewer mismatches at unique positions were retained. Iteratively, one base was discarded form the 3`end of the nonmapped reads until the reads were uniquelly mapped or fell bellow a minimum length of 30 bp
Peaks were detected using CSAR
Genome_build: Arabidopsis TAIR9
Supplementary_files_format_and_content: Location of peaks and their associated score enrichment are reported in the processed data

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Arabidopsis pistil/silique stage 12-16

growth_protocol: The plants were grown on soil at 22 °C under long day condition (16 h light, 8 h dark).

extract_protocol:
ChIP experiments were performed according to a previously published protocol (Kaufmann et al., Nature Protocols, 2010) using a GFP antibody. Approximately 1 g of pistils/siliques were used for each biological replicate. The input sample was used as negative control.
Libraries were prepared using the Illumina protocol for preparation of ChIP-SEQ libraries with modifications described in Kaufmann et al., Nature Protocols 2010

treatment_protocol: Sample collection was laborious and tissue was harvested throughout the day. No specific treatment was applied.

tag: ecotype

value: Col/Ler

tag: genotype

value: pFUL:FUL-GFP ful-1

value: pistil/silique

tag: developmental stage

value: stage 12-16

tag: antibody

value: none, input control


title: Input DNA of replicate 2 (GBY-1)


title: FUL-GFP in ful-1, replicate 2

value: GFP


title: Pha_ex_1

description: tRNA


title: Bsu_ex_2

description: tRNA


title: FUL-GFP in ful-1, replicate 1


title: Pha_sta_3

description: tRNA


title: Pha_sta_1

description: tRNA


title: Bsu_sta_2

description: tRNA


title: Bsu_ex_1

description: tRNA


title: Smad4_mES_day3EB_Ab40759

city: Hangzhou

first: Yilong

last: Zou

state: Zhejiang

address: Shilongshan Road #18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake University

description: ChIP-Seq

data_processing:
Sequencing data quality control: Sequencing reads in FASTQ format were quality assessed by FastQC v0.11.3 for sequencing integrity and completeness
Read mapping: FASTQ reads were mapped to mouse genome mm9 (NCBI build 37, Jul/2007) with Bowtie2 with default filtering criteria. Resulted SAM files were converted to BAM files though Samtools 0.1.19. BAM files were sorted and indexed with Samtools.
ChIP-Seq data visualization: To visualize ChIP-Seq data, BAM files were converted to TDF file by IGV Tools 2.3.32 using the command “igvtools count -z 5 -w 25 -e 250”, specifying the coverage window size to be 25bp and average fragment size of 250bp.
Genome_build: mm9, NCBI build 37, July/2007
Supplementary_files_format_and_content: TDF files are contain whole-genome coverage data for eac ChIP-Seq sample. This file data can be loaded to IGV genome browser and visualize ChIP-Seq peak distribution.

source_name: mouse embroid bodies

growth_protocol: mESCs E14Tg2a.IV were maintained on gelatin (0.1%, Millipore, ES-006-B) coated plates with LIF-supplemented medium at 37°C with 5% CO2. Basic ES cell medium included 80% Knockout DMEM (Life Technologies, 10829-018), 15% Fetal Bovine Serum (HyClone, SH30071), 50U Penicillin and 50ug/ml Streptomycin (Cellgro, 30-001-CI), 1% Non-essential Amino acids (Life Technologies, 11140-050), 1% L-Glutamine (Life Technologies, 25030081), 100μM β-Mercaptoethanol (Sigma-Aldrich, M6250), 1000 U/ml mLIF (Gemini Bio-Products, 400-495). EB formation and differentiation were carried out as described by the supplier (ATCC).

extract_protocol:
mouse EBs are treated with Activin, fixed and quenched, sonicated to average fragment size of 250bp in 1% SDS lysis buffer, and incubated with 60ul Dynabeads protein G conjugated with 3-5ug of indicated antibodies. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. Magnetic beads were washed, chromatin was eluted, and reverse crosslinked ChIP DNA was dissolved in 10 mM Tris pH 8.0 buffer for further analysis.
ChIP-Seq DNA samples were quantified and quality assessed by Ribogreen and Agilent Bioanalyzer. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.
Multiplexed sequencing libraries were ran on a Hiseq2500 platform.

treatment_protocol: Recombinant human Activin A (R&D Systems, 338-AC) were used at 50ng/ml.

tag: genetic background

value: wild type

tag: vendor

value: Abcam

tag: catalog #


title: ATACseq_SCC3_Tgfbr2KO_A

status: Public on Nov 02 2017

city: New York

first: Markus

last: Schober

state: NY

address: 550 First Ave, Smilow 407

department: Dermatology

institute: New York University School of Medicine

data_processing:
Mouse assembly version mm10/NCBI m38 build were used for sequence alignments with bowtie 45 version 2.1.0.
ATAC-seq peaks were called with PeaKDEck55 and the parameter (-sig 0.0001).
Genome_build: mm10

source_name: squamous cell carcinoma

growth_protocol: 10,000 cells were injected intradermally to form tumor allografts

extract_protocol:
50,000  TPCs were isolated by FACS and washed once with cold 1x PBS. Cells were pelleted and lysed in 50 μl and spun at 500g for 6min at 4C to collect nuclei.
Pelleted nuclei were incubated for 30min at 37 C with Tn5 transposase (Illumina Cat #FC-121-1030) before transposed DNA fragments were purified with a Qiagen MinElute Kit for ATAC-seq library generation.

tag: genotype/variation

value: skin

tag: cell type

value: squamous cell carcinoma


title: ChIPseq_Input_SCC2

data_processing:
Mouse assembly version mm10/NCBI m38 build were used for sequence alignments with bowtie 45 version 2.1.0.
Sequences with MAPQ scores <30 were removed with samtools50 and duplicates were removed with picard-tools version 1.88
IGV viewer files were generated with igvtools count -z 5 -w 25 -e 250.
ChIP-seq peaks were called with MACS51 version 2.1.0 in comparison to input controls with the parameters -q 0.001 --nomodel --extsize 400.
Motif discovery was performed with MEME-ChIP52,53 using 200bp sequence surrounding peak summits.
Motif containing ChIP-seq peaks were analyzed with the GREAT: Genomic Regions Enrichment of Annotations Tool54, using default parameters.
Genome_build: mm10

growth_protocol: Cells were grown in low calcium (50uM) conditions

extract_protocol:
Chromatin was prepared from 12x10^6 SCC cells using the ChIP-IT High Sensitivity kit (53040, Active Motif) according to manufacturers instructions.
Library prep was performed with the Rubicon ThruPLEX DNA-seq kit according to manufacturers instructions.

treatment_protocol: Cells were treated for 1hr with 5ng/mL TGFβ1

tag: strain


title: Smad4_mES_day3EB_SC7966

description: ChIP-Seq

value: Santa Cruz Biotechnology


title: Bsu_sta_1

description: tRNA


title: ATACseq_SCC3_Tgfbr2KO_B

tag: tissue


title: RNAseq_SCC2_CD71lo_H2BGFPlo

data_processing:
Analysis was performed using tophat (version 2.0.9) for read alignment (default parameters)
Cufflinks (version 2.2.0) for transcriptome assembly (with parameters  --no-coverage-search and --no-novel-juncs)
Cuffdiff (version 2.2.0) for identifying differentially expressed genes (default parameters)
Mouse assembly mm9 was used and transcriptome annotations were obtained from ENSEMBL release 69.
Genome_build: mm10

extract_protocol:
Total RNA was extracted from 1x10^5 sorted SCC cells using the Absolutely RNA Nanoprep Kit (400753, Agilent Technologies) according to manufacturers instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell population

value: double negative CD71lo H2BGFPlo


title: RNASeq_SCC1_CD71lo_H2BGFPlo


title: M1- MEDIP-seq

city: Kunming

first: XiaoMing

last: Dai

state: Yunnan

address: 293#,Xichang road

department: The maxillofacial service of the department of plastic surgery,

institute: The first affiliated hospital of Kunming Medical University

data_processing:
Image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8)
After passing Solexa CHASTITY quality filter, the clean reads were aligned to mouse genome (UCSC MM10) using BOWTIE software (V2.1.0)
Data were filtered using the following specification: Individual bases generated from original image files have quality scores which reflect the probability whether a base-call is correct or not. The score is calculated by CHASTITY Formula.  The CHASTITY(C) of each base in the short reads is determined by the intensity of four colors (IA, IC, IG, IT here), and the formula means “the ratio of the highest (IC here) of the four (base type) intensities to the sum of highest two (IC and IG here).” The CHASTITY(C) should be no less than 0.6 in the first 25 bases.
Genome_build: UCSC MM10
Supplementary_files_format_and_content: To quantify the DNA methylation level of any specific region. A methylation score for any region in the genome was defined as number of extended reads per kb (according to A.K. Maunakea et al, 2010)

source_name: early stage during lingual tumorigenesis

extract_protocol:
genomic DNA was extracted and purified from lingual mucosa samples using Qiagen DNeasy Kit according to standard instructions
Genomic DNA was sonicated to ~200 - 900bp fragments, and 1 μg of fragmented sample was ligated to Illumina’s genomic adapters with Genomic DNA Sample Kit (#FC-102-1002, Illumina), following the manufacturer’s instructions. ~300 - 1000 bp ligated DNA fragments were further immunoprecipitated by anti-5-methylcytosine antibody (Diagenode). The enriched DNA was amplified by PCR and purified by agarose gel. QC was performed to assess the quality of MeDIP experiment and sequencing library.
methylated DNA Immunoprecipitation sequencing

treatment_protocol: 4-NQO was obtained from Sigma-Aldrich Co. LLC. (U.S.A), dissolved in propylene glycol to a concentration of 500mg/L for storage. 4NQO in drinking water at a dose of 50mg/L for was delivered for16weeks. Drink water was changed every week. The drinking water in all groups was then exchanged for distilled water from the 17th week to the cessation of experiment at the 28th week.

tag: Sex

value: female

value: lingual mucosa

tag: histopathological diagnosis

value: mucosa with hyperplasia, mild and moderate dysplasia

tag: chip antibody


title: E1- MEDIP-seq

source_name: advanced stage during lingual tumorigenesis

value: mucosa with carcinoma in situ and invasive cancer


title: E2- MEDIP-seq


title: E3- MEDIP-seq


title: M2- MEDIP-seq


title: C3- MEDIP-seq

source_name: normality

value: normal mucosa


title: C1- MEDIP-seq


title: C2- MEDIP-seq


title: ATACseq_SCC1_CD71hi_H2BGFPhi

description: Processed data file: all_merged_ATAC_peaks.bed

data_processing:
Library strategy: ATAC-Seq
Mouse assembly version mm10/NCBI m38 build were used for sequence alignments with bowtie 45 version 2.1.0.
ATAC-seq peaks were called with PeaKDEck55 and the parameter (-sig 0.0001).
genome build: mm10

extract_protocol:
50,000  TPCs were isolated by FACS and washed once with cold 1x PBS. Cells were pelleted and lysed in 50 μl and spun at 500g for 6min at 4C to collect nuclei. Pelleted nuclei were incubated for 30min at 37 C with Tn5 transposase (Illumina Cat #FC-121-1030) before transposed DNA fragments were purified with a Qiagen MinElute Kit for ATAC-seq library generation.
Library construction protocol not provided.

value: CD71hi H2BGFPhi


title: ATACseq_SCC1_CD71lo_H2BGFPhi

value: CD71lo H2BGFPhi

tag: phenotype

value: quiescent


title: ATACseq_SCC1_CD71hi_H2BGFPlo

value: CD71hi H2BGFPlo

value: proliferative


title: ATACseq_SCC1_CD71lo_H2BGFPlo

value: CD71lo H2BGFPlo


title: Pha_sta_2

description: tRNA


title: ATACseq_SCC2_CD71lo_H2BGFPlo


title: ATACseq_SCC2_CD71hi_H2BGFPlo


title: ATACseq_SCC2_CD71lo_H2BGFPhi


title: M3- MEDIP-seq


title: ChIPseq_Smad2/3_SCC1

description: Processed data file: Smad23_bound_with_motif.bed

data_processing:
Mouse assembly version mm10/NCBI m38 build were used for sequence alignments with bowtie 45 version 2.1.0.
Sequences with MAPQ scores <30 were removed with samtools50 and duplicates were removed with picard-tools version 1.88
IGV viewer files were generated with igvtools count -z 5 -w 25 -e 250.
ChIP-seq peaks were called with MACS51 version 2.1.0 in comparison to input controls with the parameters -q 0.001 --nomodel --extsize 400.
Motif discovery was performed with MEME-ChIP52,53 using 200bp sequence surrounding peak summits.
Motif containing ChIP-seq peaks were analyzed with the GREAT: Genomic Regions Enrichment of Annotations Tool54, using default parameters.
genome build: mm10

growth_protocol:
Cells were grown in low calcium (50uM) conditions
Cells were treated for 1hr with 5ng/mL TGFβ1


title: Day3 Smad3CA+ Dox- Smad3 Rep3

city: Edinburgh

first: Keisuke

last: Kaji

state: Midlothian

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

country: United Kingdom

institute: University of Edinburgh

description:
Processed data file: D3_3CA_NoDox_Smad3.tab.gz
Processed data file: D3_3CA_NoDox_Smad3.bigwig
Processed data file: D3_3CA_NoDox_Smad3.gappedPeak.gz
Processed data file: D3_3CA_NoDox_Smad3.broadPeak.gz
Processed data file: D3_3CA_NoDox_Smad3_Rep3.gappedPeak.gz
Processed data file: D3_3CA_NoDox_Smad3_Rep3.broadPeak.gz

data_processing:
Reads were quality-checked using FastQC version 0.11.5.
Reads were trimmed using Trimmomatic version 0.36.
Reads were aligned to the mm10 genome assembly using Bowtie2 version 2.28.
Duplicate reads were removed using MarkDuplicates from Picard Tools version 2.3.0.
Reads were filtered for MAPQ >= 40 using SAMtools version 1.3.
Reads aligned to the ENCODE blacklist region were removed using BEDtools version 2.25.0.
Peaks were called using MACS2 version 2.1.0.
BigWig files were generated using BamCompare from DeepTools version 2.2.3.
Heatmaps were generated using computeMatrix and plotHeatmap from DeepTools version 2.2.3.
Differentially bound sites were obtained using DiffBind version 1.16.3.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Peak-calling files in narrowPeak, broadPeak, and gappedPeak formats were generated using MACS2 version 2.1.0.
Supplementary_files_format_and_content: Tab-delimited text and bigWig files of Input-subtracted ChIP-factor read counts / density were generated using BamCompare, computeMatrix, and plotHeatmap from DeepTools version 2.2.3.
Supplementary_files_format_and_content: Tab-delimited text files of differentially bound sites were generated using DiffBind version 1.16.3.

source_name: Mouse embryonic fibroblasts, Smad3CA+, Dox-, day 3 of reprogramming, Smad3 ChIP

growth_protocol: Mouse embryonic fibroblasts (MEFs) with doxycycline-inducible MKOS were cultured in ESC medium (Glasgow's Minimum Essential Medium (GMEM), 10% FCS, non-essential amino acids, 2 mM L-Glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin/streptomycin, all from Life Technologies) supplemented with human LIF 100 U/ml) in the presence or absence of 1 μg/ml doxycycline after retroviral Smad3CA expression vector infection.

extract_protocol:
A pellet of ~2x10^6 cells was thawed and nuclei were isolated by re-suspension in lysis buffer (5 mM Pipes pH 8.0, 85 mM KCl, 1% NP40) with fresh protease inhibitors (complete protease inhibitor cocktail, Roche) for 20 minutes on ice followed by brief vortexing and centrifugation at 500 g for 10 minutes at 4 °C. The nuclear pellet was re-suspended in 300 ul IP buffer (0.5% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, fresh protease inhibitors) and sonicated to produce ~200-300 bp fragments in a BioRuptor Sonicator with a total of 5-8 cycles of: 10 pulses of sonication on the “high” setting, each followed by 30 seconds off. Thus, each sample received between 50-80 pulses of 30-second 'high' sonication. Samples were then diluted in IP buffer without SDS (to final 0.1% SDS), then 8 µg antibody was added for overnight incubation, rotating at 4 °C.
ChIP'd DNA from ~2x10^6 cells was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters, which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for total 16-18 cycles and library fragments of ~250 bp were isolated with SeraMag beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: +/- 1 μg/ml doxycycline

value: Mouse embryonic fibroblasts

tag: smad3ca expression

value: present

tag: dox treatment

value: Dox-

tag: time

value: day 3 of reprogramming


title: ChIPseq_Input_SCC1

value: skin


title: Day3 Smad3CA+ Dox+ Smad3 Rep2

description:
Processed data file: D3_3CA_Dox_Smad3.tab.gz
Processed data file: D3_3CA_Dox_Smad3.bigwig
Processed data file: D3_3CA_Dox_Smad3.gappedPeak.gz
Processed data file: D3_3CA_Dox_Smad3.broadPeak.gz
Processed data file: D3_3CA_Dox_Smad3_Rep2.gappedPeak.gz
Processed data file: D3_3CA_Dox_Smad3_Rep2.broadPeak.gz

source_name: Mouse embryonic fibroblasts, Smad3CA+, Dox+, day 3 of reprogramming, Smad3 ChIP

value: Dox+


title: Day3 Smad3CA+ Dox+ Smad3 Rep1

description:
Processed data file: D3_3CA_Dox_Smad3.tab.gz
Processed data file: D3_3CA_Dox_Smad3.bigwig
Processed data file: D3_3CA_Dox_Smad3.gappedPeak.gz
Processed data file: D3_3CA_Dox_Smad3.broadPeak.gz
Processed data file: D3_3CA_Dox_Smad3_Rep1.gappedPeak.gz
Processed data file: D3_3CA_Dox_Smad3_Rep1.broadPeak.gz


title: ATACseq_SCC2_CD71hi_H2BGFPhi


title: Day3 Smad3CA+ Dox+ Input Rep1

source_name: Mouse embryonic fibroblasts, Smad3CA+, Dox+, day 3 of reprogramming, Input


title: Day3 Smad3CA+ Dox- Input Rep2

source_name: Mouse embryonic fibroblasts, Smad3CA+, Dox-, day 3 of reprogramming, Input


title: Day3 Smad3CA+ Dox- Input Rep1


title: Day3 Smad3CA+ Dox+ Input Rep2


title: Day3 Smad3CA+ Dox+ Oct4 Rep2

description:
Processed data file: D3_3CA_Dox_Oct4.tab.gz
Processed data file: D3_3CA_Dox_Oct4.bigwig
Processed data file: D3_3CA_Dox_Oct4.narrowPeak.gz
Processed data file: D3_3CA_Dox_Oct4_Rep2.narrowPeak.gz

source_name: Mouse embryonic fibroblasts, Smad3CA+, Dox+, day 3 of reprogramming, Oct4 ChIP


title: Day3 Smad3CA+ Dox- Smad3 Rep2

description:
Processed data file: D3_3CA_NoDox_Smad3.tab.gz
Processed data file: D3_3CA_NoDox_Smad3.bigwig
Processed data file: D3_3CA_NoDox_Smad3.gappedPeak.gz
Processed data file: D3_3CA_NoDox_Smad3.broadPeak.gz
Processed data file: D3_3CA_NoDox_Smad3_Rep2.gappedPeak.gz
Processed data file: D3_3CA_NoDox_Smad3_Rep2.broadPeak.gz


title: Day3 Smad3CA+ Dox- Smad3 Rep1

description:
Processed data file: D3_3CA_NoDox_Smad3.tab.gz
Processed data file: D3_3CA_NoDox_Smad3.bigwig
Processed data file: D3_3CA_NoDox_Smad3.gappedPeak.gz
Processed data file: D3_3CA_NoDox_Smad3.broadPeak.gz
Processed data file: D3_3CA_NoDox_Smad3_Rep1.gappedPeak.gz
Processed data file: D3_3CA_NoDox_Smad3_Rep1.broadPeak.gz


title: Day3 Smad3CA+ Dox+ Oct4 Rep3

description:
Processed data file: D3_3CA_Dox_Oct4.tab.gz
Processed data file: D3_3CA_Dox_Oct4.bigwig
Processed data file: D3_3CA_Dox_Oct4.narrowPeak.gz
Processed data file: D3_3CA_Dox_Oct4_Rep3.narrowPeak.gz


title: Day3 Smad3CA+ Dox+ Oct4 Rep1

description:
Processed data file: D3_3CA_Dox_Oct4.tab.gz
Processed data file: D3_3CA_Dox_Oct4.bigwig
Processed data file: D3_3CA_Dox_Oct4.narrowPeak.gz
Processed data file: D3_3CA_Dox_Oct4_Rep1.narrowPeak.gz


title: MEF Rep2

description:
ATAC-seq of mouse embryonic fibroblasts.
Processed data file: Sample_MEF.tab.gz
Processed data file: Sample_MEF.bigwig

data_processing:
Library strategy: ATAC-Seq
Reads were quality-checked using FastQC version 0.11.5.
Reads were trimmed using Trimmomatic version 0.36.
Reads were aligned to the mm10 genome assembly using Bowtie2 version 2.28 with the --very-sensitive and -X 2000 options specified.
Duplicate reads were removed using MarkDuplicates from Picard Tools version 2.3.0.
Reads were filtered for MAPQ >= 40 and properly-paired (0x2) flag using SAMtools version 1.3.
Reads aligned to the ENCODE blacklist and mitochondrial blacklist regions were removed using BEDtools version 2.25.0.
BigWig files were generated using BamCoverage from DeepTools version 2.2.3.
Heatmaps were generated using computeMatrix and plotHeatmap from DeepTools version 2.2.3.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text and bigWig files of ATAC-seq read counts / density were generated using BamCoverage, computeMatrix, and plotHeatmap from DeepTools version 2.2.3.

source_name: Mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) with doxycycline-inducible MKOS were cultured in ESC medium (Glasgow's Minimum Essential Medium (GMEM), 10% FCS, non-essential amino acids, 2 mM L-Glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin/streptomycin, all from Life Technologies) supplemented with human LIF 100 U/ml) in the presence of 1 μg/ml doxycycline after retroviral Smad3CA expression vector or control BFP vector infection.

extract_protocol:
ATAC-seq was performed according to the published protocol (Buenrostro et al., 2013). For library preparation, 50,000 cells were FACSd into PBS, and then nuclei were isolated by re-suspending the cells in lysis buffer (10mM Tris-HCl ph 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40) for 15 minutes on ice, followed by centrifugation at 500g for 10 minutes at 4oC.
Precipitated nuclei were tagmented by re-suspension in the Nextera transposase mix (22.5uL ddH2O, 25uL 2x Tagment DNA buffer, 2.5ul Tagment DNA enyme) (Nextera DNA sample prep kit, FC-121-1030 and FC-121-1011) and incubated at 37oC for 30 minutes. The tagmentation reactions were terminated and cleaned-up using Qiagen Minelute enzyme cleanup kit, eluting in a final volume of 10μl ddH2O. The fragments were amplified by PCR for ~16 cycles, and >100 bp fragments were purified with SeraMag beads.

treatment_protocol: +Smad3CA or +BFP


title: Day3 Smad3CA+ Dox+ Smad3 Rep3

description:
Processed data file: D3_3CA_Dox_Smad3.tab.gz
Processed data file: D3_3CA_Dox_Smad3.bigwig
Processed data file: D3_3CA_Dox_Smad3.gappedPeak.gz
Processed data file: D3_3CA_Dox_Smad3.broadPeak.gz
Processed data file: D3_3CA_Dox_Smad3_Rep3.gappedPeak.gz
Processed data file: D3_3CA_Dox_Smad3_Rep3.broadPeak.gz


title: MEF Rep3


title: MEF Rep1


title: D3 BFP Rep2

description:
ATAC-seq of mouse embryonic fibroblasts on day 3 of reprogramming, in the absence of Smad3CA expression.
Processed data file: Sample_D3_BFP.tab.gz
Processed data file: Sample_D3_BFP.bigwig

source_name: Mouse embryonic fibroblasts, absence of Smad3CA expression, day 3 of reprogramming

value: absent


title: D3 BFP Rep1


title: D3 3CA Rep2

description:
ATAC-seq of mouse embryonic fibroblasts on day 3 of reprogramming, in the presence of Smad3CA expression.
Processed data file: Sample_D3_3CA.tab.gz
Processed data file: Sample_D3_3CA.bigwig

source_name: Mouse embryonic fibroblasts, presence of Smad3CA expression, day 3 of reprogramming


title: D3 BFP Rep3


title: RNAseq_SCC1_CD71hi_H2BGFPlo

description: Processed data file:Genes_differentially_expressed_between_qTPCs_and_pTPCs.txt

data_processing:
Analysis was performed using tophat (version 2.0.9) for read alignment (default parameters)
Cufflinks (version 2.2.0) for transcriptome assembly (with parameters  --no-coverage-search and --no-novel-juncs)
Cuffdiff (version 2.2.0) for identifying differentially expressed genes (default parameters)
Mouse assembly mm10 was used and transcriptome annotations were obtained from ENSEMBL release 69.
Genome_build: mm10


title: RNAseq_SCC1_CD71lo_H2BGFPhi


title: RNAseq_SCC2_CD71hi_H2BGFPlo


title: RNAseq_SCC2_CD71lo_H2BGFPhi


title: d10_BFP2 [H05]

data_processing:
Sequenced reads were preprocessed as described in Islam et al 2014 (doi:10.1038/nmeth.2772). Briefly, reads were trimmed to remove 3' bases with a quality score of B and to extract barcode sequences. Reads with < 25 transcript derived bases not include 3' poly-A sequences were removed. Up to 9 Gs were removed from the 5' end of the transcript derived sequence (likely to be derived from template-switching). Reads of < 6 non-A bases at the end of this process were discarded. The transcript derived part of the read after this process was therefore around 42bp, but of variable length.
Reads were aligned to the mm10 genome using the bowtie1 aligner version 0.12.9 , allowing <=3 mismatches. Non-mapped reads are tried against a splice junction chromosome.
Reads with more than 25 alternative mappings were discarded prior to downstream analyses. Other multiple-mapping reads were randomly assigned to a genomic position. For generating counts per feature (UCSC gene), reads were assigned to the transcript where the position is closest to the 5' end. The molecular tags (UMIs) produced by the STRT platform were not used in our analysis.
Read counts were normalised and processed for differential expression with DESeq2 v.1.6.3
Genome_build: mm10
Supplementary_files_format_and_content: A single tab-delimited text file shows the raw counts for each sample

growth_protocol: Cells were reprogrammed in ES media: Glasgow's Minimum Essential Medium (GMEM), 10% FCS, non-essential amino acids, 2 mM L-Glutamine, 1 mM sodium pyruvate, 100 U/ml penicillin/streptomycin, all from Life technologies plus 100U/ml LIF),  supplemented with Doycycline (300ng/ml) and VitaminC (10mg/ml). MEF were grown in ES media without LIF, with addition of 5 ng/ml FGF2 and 1 ng/ml heparin

extract_protocol:
Cell were harvested with trypsin, flow sorted, then snap frozen in PBS with RNAse inhibitor. Cells were prepared for RNA extraction by lysing  with 0.15% Triton X-100, 1 U/μL TaKaRa RNase inhibitor, 4 μM reverse transcription primer C1-P1-T31, 5% C1 Loading Reagent and 1:50,000 Life Technologies ERCC Spike-In Mix 1
Reverse transcription mix: 1× SuperScript II First-Strand Buffer supplemented with 3 mM MgCl2, 1.5 mM dNTP, 4 mM DTT, 3.3% C1 Loading Reagent, 1.8 μM template-switching oligo C1-P1-RNA-TSO, 1.5 U/μL TaKaRa RNase inhibitor and 18 U/μL Life Technologies Superscript II reverse transcriptase. PCR mix: (1.1× Clontech Advantage2 PCR buffer, 440 μM dNTP, 530 nM PCR primer C1-P1-PCR-2, 5% C1 Loading Reagent and 2× Advantage2 Polymerase Mix

tag: strain background

tag: group

value: BFP

tag: days from start of reprogramming


title: d10_BFP3 [H06]


title: d10_BFP1 [H04]


title: d10_Sm3CA3 [H03]


title: d10_Sm3CA1 [H01]


title: d10_BFP2 [G05]


title: d10_BFP3 [G06]


title: d10_Sm3CA2 [H02]


title: D3 3CA Rep1


title: d8_Sm3CA2 [F08]


title: d10_Sm3CA1 [G01]


title: d8_Sm3CA3 [F09]


title: d8_Sm3CA1 [F07]


title: d8_BFP3 [F12]


title: d6_BFP3 [F06]


title: d8_BFP1 [F10]


title: d10_Sm3CA2 [G02]


title: d6_BFP2 [F05]


title: d8_BFP2 [F11]


title: d6_BFP1 [F04]


title: d8_BFP2 [E11]


title: d6_Sm3CA2 [F02]


title: d10_Sm3CA3 [G03]


title: d6_Sm3CA1 [F01]


title: d8_BFP3 [E12]


title: d8_Sm3CA3 [E09]


title: d8_BFP1 [E10]


title: d10_BFP1 [G04]


title: d6_BFP2 [E05]


title: d8_Sm3CA1 [E07]


title: d6_BFP3 [E06]


title: d8_Sm3CA2 [E08]


title: d6_BFP1 [E04]


title: d6_Sm3CA3 [E03]


title: d6_Sm3CA1 [E01]


title: d8_BFP2 [D11]


title: d8_BFP3 [D12]


title: d6_Sm3CA2 [E02]


title: d6_Sm3CA3 [F03]


title: d8_BFP1 [D10]


title: d8_Sm3CA3 [D09]


title: d6_BFP3 [D06]


title: d6_BFP1 [D04]


title: d8_Sm3CA2 [D08]


title: d6_Sm3CA1 [D01]


title: d6_Sm3CA2 [D02]


title: d6_Sm3CA3 [D03]


title: d8_Sm3CA1 [D07]


title: d3_BFP3 [C12]


title: ES2 [C05]

source_name: MES

value: Mouse embryonic stem cells

value: ES


title: d3_Sm3CA1 [C07]


title: ES1 [C04]


title: Mef3 [C03]

source_name: MEFs

value: Mef


title: ES3 [C06]


title: d3_BFP1 [B10]


title: d3_BFP3 [B12]


title: Mef2 [C02]


title: d6_BFP2 [D05]


title: d3_BFP2 [C11]


title: ES3 [B06]


title: d3_Sm3CA1 [B07]


title: d3_Sm3CA2 [B08]


title: d3_BFP1 [C10]


title: d3_Sm3CA3 [C09]


title: d3_Sm3CA3 [B09]


title: d3_Sm3CA2 [C08]


title: d3_BFP2 [B11]


title: Mef1 [C01]


title: ES1 [B04]


title: ES2 [B05]


title: Mef1 [B01]


title: d3_BFP3 [A12]


title: d3_BFP2 [A11]


title: d3_Sm3CA3 [A09]


title: d3_BFP1 [A10]


title: d3_Sm3CA1 [A07]


title: ES3 [A06]


title: DOX_2

city: Lausanne

first: Xu

last: Wang

address: EPFL SV IBI-SV NCEM AI 1148 (Bâtiment AI) Station 15

country: Switzerland

institute: École polytechnique fédérale de Lausanne

data_processing:
Raw FASTQ files generated were subjected to quality control analysis by using FastQC v0.10.1. The reads were then mapped against the Arabidopsis thaliana genome (TAIR10) with TopHat2.0.14. Cufflinks v2.2.1 was then used to obtain normalized FPKM expression for each annotated gene.
Genome_build: TAIR10
Supplementary_files_format_and_content: The tab-delimited text files include FPKM values for each gene.

molecule: polyA RNA

source_name: seedling DOX

growth_protocol: Wild type and mrpl1 mutant plants were grown for 14 days on solid 1/2 MS medium.

extract_protocol:
Total RNA from these seedlings were prepared using RNeasy Plant Mini Kit and (QIAGEN). 1 µg of total RNA was enriched for Poly-A RNA using the Ambion Dyna mRNA Micro Poly (A) kit according to manufacturer’s standard protocol.
The libraries for sequencing were prepared using the Ion Total RNAseq v2 kit and the Ion Xpress 1-48 Barcode kit. Libraries were amplified 16 cycles and the quality of the libraries was checked on an Agilent Bioanalyzer DNA High Sensitivity chip. 1 µl of each sample was pooled and sequenced on an Ion Torrent PGM 314 chip. The libraries were re-pooled based on reads from the PGM 314 chip, purified on a Pippin Prep gel, quantified by the Agilent Bioanalyzer and sequenced on an Ion Torrent Proton sequencer.

treatment_protocol: 10 ml of liquid 1/2 MS medium supplemented with 0 or 25 μg/ml doxycycline were added into the petri dishes holding wild type plants. Meanwhile, to keep the same condition, the same liquid medium, but without doxycycline, was also supplied to the mrpl1 mutant plants. The treatment lasted for 12 h in the light cycle.

tag: ecotype

value: wild type

value: seedling

tag: treatment

value: half MS plus 25 μg/ml doxycycline


title: DOX_3

tag: genotype/variation


title: Mef3 [B03]

tag: cell type


title: ES2 [A05]


title: DOX_1


title: WT_control_1

source_name: seedling WT_control

value: half MS


title: mrpl1-1_3

source_name: seedling mrpl1-1

growth_protocol: Wild type and mrpl1-1 mutant plants were grown for 14 days on solid 1/2 MS medium.

treatment_protocol: 10 ml of liquid 1/2 MS medium supplemented with 0 or 25 μg/ml doxycycline were added into the petri dishes holding wild type plants. Meanwhile, to keep the same condition, the same liquid medium, but without doxycycline, was also supplied to the mrpl1-1 mutant plants. The treatment lasted for 12 h in the light cycle.

value: mrpl1-1 mutant


title: WT_control_3


title: WT_control_2


title: Mef3 [A03]


title: ES1 [A04]


title: Patient 7, day 2292

city: Madrid

first: Paloma

last: Talayero

address: Avenida de Cordoba s/n

department: Immunology

country: Spain

institute: Hospital 12 de Octubre

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adapter sequence and low-quality sequences using Cutadapt software v1.6
Clean reads were aligned to the reference human genome (Ensembl gene-build GRCh37.75) using TopHat2 v2.0.13 with parameters -g 1 –coverage-search --microexon-search --library-type fr-unstranded --b2-sensitive
Gene expression values were calculated as counts using HTSeq v0.6.1 with parameters --mode=intersection-nonempty --stranded=no --type=exon –idattr=gene_name
Genome_build: Ensembl gene-build GRCh37.75
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: ileum

extract_protocol:
Intestinal biopsies were submerged in RNAlater solution (Ambion) and stored at -80ºC until RNA extraction. After the disruption with needle and syringe and homogenization with QIAshredder (Qiagen), RNA was isolated and purified with RNeasy Mini Kit (Qiagen)
Total RNA was used with the TruSeq RNA Sample Preparation v2 Kit (Illumina)

tag: stability

value: Stable

tag: tissue type

value: ileum


title: mrpl1-1_1

tag: tissue


title: Mef2 [B02]

value: Mouse embryonic fibroblasts


title: Th2_invitro_4

city: San Francisco

first: Heather

middle: H

last: Pua

address: 513 Parnassus Ave, HSE-201, Box 0997

institute: UCSF

description:
processed data file:
MAPS04_exceRpt_miRNA_ReadCounts.csv

data_processing:
data filtering step: Adapters were trimmed and data was demultiplexed using FastX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Raw data files are provided after these processing steps, as there is no standard index read for read sorting before processing in this custom protocol.
alignment: Sequence alignments and small RNA read counts were obtained using the exceRpt small RNA-seq Pipeline (v3) (https://www.genboree.org/epigenomeatlas/genboreeWorkbench.rhtml)
expression analysis: Comparative expression analysis was performed with DESeq2 (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain raw read counts from the exceRpt small RNA-seq Pipeline. The supplementary file ILC2miRNA_DESeq2norm_rpm contains DESeq2 normalized rpm counts for each sample.

extract_protocol:
8,000-3,000,000 cells were lysed in Trizol LS (Life Technologies) and RNA isolated using a miRNAeasy Micro Kit (Qiagen).
5-50ng of total RNA from sorted and/or cultured cells were used to build miRNA libraries as previously described (PMID 23440203).

treatment_protocol: 5 day in vitro culture with anti-CD3, anti-CD28, 500U/ml IL-4 and 10ug/ml anti-IFNg

tag: genotype

value: Wild type

tag: tissue source

value: spleen and lymph nodes

value: CD4+ T lymphocytes

tag: sorting

value: CD4+ dynabead positive selection


title: Patient 8, day 1096


title: mrpl1-1_2


title: Mef1 [A01]


title: d3_Sm3CA2 [A08]


title: Th2_invitro_3

description:
processed data file:
MAPS03_exceRpt_miRNA_ReadCounts.csv


title: Patient 6, day 929


title: Mef2 [A02]


title: Th2_invitro_2

description:
processed data file:
MAPS02_exceRpt_miRNA_ReadCounts.cvs


title: Th2_invitro_1

description:
processed data file:
MAPS01_exceRpt_miRNA_ReadCounts.cvs


title: Patient 5, day 1826


title: Patient 5, day 1874


title: Th2_AA_3

treatment_protocol: 50ug OVA + alum intraperitoneal sensitization x 3 weeks, 50ug OVA oropharygeal aspiration x 3 days

value: lung


title: Patient 4, day 244


title: Th2_AA_2


title: Patient 4, day 115

value: Non stable


title: Patient 4, day 176


title: Th2_AA_1


title: Patient 4, day 90


title: CD4_4


title: CD4_3


title: CD4_2


title: Patient 3, day 125


title: Patient 3, day 185


title: Patient 6, day 1504


title: Patient 4, day 48


title: Patient 3, day 49


title: ILC2_invitro_4

treatment_protocol: 10 day in vitro culture with 10ng/ml IL-33, TSLP, and IL-7

value: Group 2 innate lymphoid cells (ILC2)


title: Patient 2, day 509


title: Patient 3, day 30


title: ILC2_invitro_1


title: Patient 2, day 134


title: ILC2_invitro_2


title: Patient 2, day 99


title: Patient 2, day 79


title: Patient 1, day 643


title: ILC2_IL33_3

treatment_protocol: 500ng IL-33 oropharyngeal aspiration x 3 days


title: ILC2_invitro_3


title: Patient 1, day 113


title: ILC2_IL33_2


title: ILC2_IL33_1


title: ILC2_4


title: Patient 2, day 33


title: Patient 1, day 33


title: ILC2_3


title: CD4_1


title: ILC2_2


title: ILC2_1


title: ALA-treated  NIH3T3

city: Fukuoka

first: Tetsuya

last: Sato

address: 3-1-1, Maidashi Higashi-ku

institute: Kyushu University

data_processing:
Read quality was checked for each sample using FASTQC version 0.11.5.
Reads of ALA +/- samples were mapped to Mus. musculus reference genome (UCSC version mm10) using TopHat version 2.1.1 with the option ‘-segment-length 20’.
The Cufflinks package version 2.2.1 with default parameters was then used to assemble the transcripts and to calculate the fragments per kilobase of exon per million mapped fragments (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: excel files include RPKM values for each sample; normalized abundance measurements

source_name: NIH3T3 cells

extract_protocol:
Total RNA was purified from NIH3T3 cells treated without or with 100μM ALA for 16 h, using the guanidium isothiocyanate method.  mRNA-seq libraries were created using the Illumina TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s standard protocol.  Samples were then subjected to single-end sequencing of 41-bp reads on the Illumina Genome Analyzer IIx.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: treated with

value: 100μM ALA for 16 h


title: ILC2_IL33_4


title: untreated NIH3T3

value: none (untreated control)


title: N2-25-Bsub-1

city: Logrono

first: María

last: de Toro

state: La Rioja

address: C/Piqueras 98

department: Genomics & Bioinformatics Core Facility

institute: Centro de Investigación Biomédica de La Rioja

data_processing:
Sequenced reads were trimmed for adaptor sequence and  low-quality sequence with TrimGalore default parameters
Clean reads were mapped to c.elegans whole genome (WBcel235.85) with Tophat2 (v2.1.1 & default parameters). Then, resulting .bam file was sorted by position and indexed with Samtools.
Bam files were processed with FeatureCounts tool (Liao et al., 2014) in order to obtain raw counts on exonic features, provided by the GTF file.
Quantitative differential expression analysis between conditions was performed both by DESeq2 (Love et al., 2014) and edgeR (Robinson et al., 2010) implementations, to compare all groups in pairs to analyze the effect of the two variables of this study: food sources (E. coli diet vs B. subtilis diet) and growth temperatures (15ºC vs 20ºC vs 25ºC). Both of them, implemented as R Bioconductor packages, perform read-count normalization by following a negative binomial distribution model. In order to automate this process and facilitate all group combination analysis, the SARTools pipeline (Varet et al., 2016) was used.
Resulting charts, containing raw and normalized data were annotated with additional data from Biomart, WormBase and the org.Ce.eg.db databases.
Gene Ontology enrichment analysis was performed for common up/down regulated genes by using clusterProfiler package (Yu et al., 2012) through its enrichGO tool.
The regularized log2 transformation (rlog) data was represented into a 2-dimension Principal Component Analysis (PCA) plot, by tacking DESeq2 expression values
Sample-to-sample Euclidean distances were calculated from the rld data and represented in a heatmap, showing the adjacent clustering information
Genome_build: WBcel235.85
Supplementary_files_format_and_content: The tab delimited files with extension .counts.txt contain raw counts data, generated with FeatureCounts software

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Wild-type nematodes and transgenic line: AY101: cIs101 [F35E12.5p::GFP + rol-6(su1006)] were obtained from the Caenorhabditis Genetic Center (CGC, University of Minesota) and immediately stored as frozen stocks to minimize the genetic drift that may happen in isolated populations growing along the time [Weber et al 2010]. Worms were thawed and grown under standard conditions (http://www.wormbook.org) on NGM plates seeded with E. coli OP50 or B. subtilis PY79 as food source, and incubated at 15ºC, 20ºC and 25ºC during at least 3 generations before starting the experiments. After that, worm populations were synchronized by “bleaching” with hypochlorite solution, maintained in M9 medium during 20 hours to allow hatching eggs and synchronization at the first larval stage (L1). Then, worms were grown at the corresponding temperatures and bacteria diet until day 1 of adulthood, at the beginning of egg laying (120h at 15ºC, 84h at 20ºC, 60h at 25ºC). To conduct experiments, 5-7 ml of distilled water was poured on to each plate of worms and gently swirled for 10 seconds to wash the worms off the plate. The water containing the worms was then transferred to a 50 ml centrifuge tube and the worms were allowed to settle to the bottom of the tube. The worms were washed with fresh distilled water 2–3 times to remove bacteria and other food sources. The worm sediment was used for the subsequent RNA extraction.

extract_protocol:
RNeasy Mini kit (Qiagen, Valencia, CA), and treated with DNase I (Qiagen) following manufacturer’s instructions.
Sequencing libraries were prepared by following the TruSeq RNA Library (LS) Preparation Kit v2 (Illumina Inc., San Diego, CA) from 500 ng of mRNA.

tag: developmental stage

value: Adult (beginning egg laying 60h)

tag: growth temperature

value: grown at 25ºC

tag: diet type

value: B.subtillis feeding


title: N2-15-Bsub-3

value: Adult (beginning egg laying 120h)

value: grown at 15ºC


title: N2-20-Bsub-2

value: Adult (beginning egg laying 84h)

value: grown at 20ºC


title: N2-15-Bsub-2


title: N2-15-Bsub-1


title: N2-20-Bsub-1


title: N2-20-Bsub-4


title: KO_IL18_1

city: Manchester

first: Santiago

last: Zelenay

state: UK

address: Alderley Park

institute: CRUK Manchester Institute

data_processing:
Basecalling was performed using Illumina bcl2fastq2 Conversion Software v2.16
Single-end sequencing reads were first trimmed using bbduk to remove the first 12 bases. A contaminant kmer discovery length of 13 was used for contaminant removal. Regions of length 20 or above with average quality of less than 10 were trimmed from the end of each read. Finally, trailing polyG and polyA were removed from the reads using cut adapt.
Trimmed reads were aligned to reference genome mm10 and assigned to features in the mm10 gene annotation using the STAR program.
Read Counts were read into R and processed using the edgeR package features were filtered to remove features with no counts
Library Sizes were normalised using the TMM normalisation in the edgeR package to produce normalised counts per million reads
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Comma separated text files include raw counts or normalized counts.

source_name: Splenic NK cells

extract_protocol:
Splenic NK cells were MACS enriched according to manufacturer’s instructions (Miltenyi Biotec). Purity of NK cells was about 90% as determined by FACS NK cells were stained (CD45-BV650, NK1.1-PE, CD3e-APC, CD11b-BV421, CD27-FITC) and sorted on a FACSAria cell sorter (BD Bioscience). Purity of was ≥ 99%. Splenic NK cells from 6 mice per genotype were pooled in pairs and stimulated with IL-18 (MBL) (20 ng/ml for 4 h). RNA was prepared using standard Qiagen protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: spleen

value: NK cells

tag: age

value: 8 weeks old


title: WT_mock_ChIP

city: Ikoma

first: Nobuo

last: Ogita

state: Nara

address: 8916-5 Takayama-cho

department: Graduate School of Biological Sciences

institute: Nara Institute of Science and Technology

data_processing:
Basecalls performed using CASAVA version 1.8.2
Alignment and peak-calling performed under StrandNGS software environment
Chip-seq reads were mapped to Arabidopsis thaliana TAIR10 genome unsing COBWeb algorithm
Peaks were called using MACS algorithm with following setting:Average Fragment Length (bp) = 150 p-value,Cutoff = 9.999999747378752E-6, Enrichment Factor = 16, Detect local biases = true
Genome_build: TAIR10
Supplementary_files_format_and_content: bam files outout from COBWeb

source_name: Col-0, whole plants, mock

growth_protocol: Arabidopsis plants were grown in liquid Murashige and Skoog (MS) medium [0.5 x MS salts, 0.5 g/l 2-(N-morpholino)ethanesulfonic acid (MES), 1% sucrose, and 1 x vitamin (pH 6.3)] with gentle shaking (70 rpm) under continuous light at 22 ˚C.

extract_protocol:
Chromatin bound to the SOG1-Myc fusion protein was precipitated with anti-Myc antibody (clone 4A6, Millipore) using Dynabeads Protein A (Thermo Fisher Scientific), according to the ChIP method (Gendrel et al., 2005) with minor modifications.
Library preparation for sequencing of precipitated DNAs was performed using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs) and a Genomic DNA Sample Prep Oligo Only Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Two-week-old plants were transferred to liquid MS medium with 15 µM zeocin and treated for 2 h.

value: whole plants

value: mock

tag: chip antibody

value: Anti-Myc Tag, clone 4A6 (Millipore, Cat. #05-724, Lot #2324563)


title: KO_IL18_2


title: KO_IL18_3


title: Patient 1, day 92

value: Stable

value: ileum


title: N2-25-Bsub-4


title: N2-20-3

value: E.coli feeding


title: WT_IL18_2

value: wild type


title: N2-25-3

value: Adult (beginning egg laying 60h)


title: WT_IL18_1


title: N2-25-2

value: grown at 25ºC


title: N2-25-1


title: N2-25-Bsub-2

value: B.subtillis feeding


title: N2-20-2


title: N2-20-1


title: KO_CTR_2


title: SOG1-Myc_zeocin_ChIP

source_name: Col-0 SOG1-Myc, whole plants, zeocin

value: Col-0 ProSOG:SOG1-Myc

tag: treatment

value: 15 µM zeocin


title: N2-15-3

value: Adult (beginning egg laying 120h)

value: grown at 15ºC


title: KO_CTR_1

value: spleen


title: N2-15-2


title: WT_CTR_3

value: NK cells


title: N2-15-1


title: WT_CTR_2

value: 8 weeks old


title: 48h_G401_Clof_2

city: Paris

first: Mamy

middle: Jean de Dieu

last: ANDRIANTERANAGNA

state: Ile de France

address: 26 rue d'Ulm

department: Centre de Recherche

country: France

institute: Institut Curie

data_processing:
mapping using Tophat,  v2.0.6, Method : Global alignment - No mismatch in seed alignment (of size 22), 3 mismatches in read length, Algorithm used: Keep uniques best hits, Library type: fr-unstranded
counting using FeatureCounts, Subread v1.5.1, count fragments, ignore duplicates, feature : exon, metafeature : gene, annotation file: RefSeq
Genome_build: hg19
Supplementary_files_format_and_content: fragment counts at gene level, tab delimited format

source_name: G401 cell line

extract_protocol: TruSeq Stranded mRNA


title: WT_CTR_1


title: WT_IL18_3


title: v65.input.del.mll4.set

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm9, hg19, and dm3 genomes using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to the UCSC hg19 and dm3 genomes using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: dm3, mm9, hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: Cells were cultures in DMEM containing 10% FBS

extract_protocol:
RNA was extracted using Trizol reagent (Life technologies). RNAse free DNaseI (Sigma) was used to eliminate DNA contamination and the treated RNA was purified with RNeasy mini kit (Qiagen).
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin were sonicated using a E220 focused-ultrasonicator (Covaris). 100 µg sheared chromatin, 5 µg antibody, and 50 µl protein A/G beads (Santa Cruz) were used for each immunoprecipitation. Immunoprecipitated DNA were purified after washing, eluting, and reverse-croslinking and submitted for library preparation.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit

tag: genotype/variation

tag: shRNA

value: ChIP-Input


title: v65.input.rep1

treatment_protocol: Cells were cultures in DMEM containing 10% FBS


title: v65.h3k4me3.mll2.crispr


title: 48h_G401_DMSO_2


title: 48h_G401_DMSO_3


title: 48h_DEV_Clof_3

source_name: DEV cell line

value: DEV


title: 48h_G401_DMSO_1


title: v65.h3k4me3.del.mll4.set


title: v65.h3k4me2.mll2.crispr


title: v65.h3k4me3


title: 48h_DEV_DMSO_3


title: KO_CTR_3

tag: cell type


title: v65.h3k4me2.del.mll4.set


title: v65.h3k4me2


title: 48h_DEV_DMSO_2


title: 48h_DEV_DMSO_1


title: v65.h3k4me1.mll2.crispr


title: v65.h3k4me1.del.mll4.set


title: 48h_G401_Clof_3


title: 48h_G401_Clof_1


title: v65.input.mll2.crispr


title: v65.h3k27ac


title: v65.h3k4me1


title: v65.brwd2.833.del.mll4.set

value: BRWD2 833


title: v65.brwd2.833.mll2.crispr


title: v65.brwd2.833


title: 48h_DEV_Clof_2


title: H3K27me3 WT low Pi rep1

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome using Bowtie2
Abundance of ChIP-seq was generated using bamCoverage in deeptools packages
Genome_build: TAIR10
Supplementary_files_format_and_content: Bigwig format

growth_protocol: Seeds were sown on Petri plates and stratified for 1 d at 4C in the dark and then transferred to a growth chamber at 21C under continuous illumination (70 µmol m-2s-1). Plant roots were harvested 14 d after germination for both methylome and RNA-seq library construction.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed using root (~1.5g) of A. thaliana (Col) following the published protocols (Anne-Valérie at al., 2005; http://www.nature.com/nmeth/journal/v2/n3/full/nmeth0305-213.html). For immunoprecipitation, 5 μg of antibodies against H3K4me3 (Ab8580; Abcam) and H3K27me3 (07-499; Upstate), were used for ~25μg of chromatin extracts. DNA was purified using MinElute PCR purification kit (QIAGEN) for sequencing libraries preparation.
DNA was quantified by Qubit and analyzed by bioanalyzer 2100. 2-5 ng ChIPed DNA was used to made ChIP-seq library. Libraries for ChIP-seq were prepared following KAPA Library Preparation Kits Illumina series (#KK8201, KAPA Biosystems) according to the manufacture’s protocol.

tag: culture condition

value: high Pi

value: root


title: 48h_DEV_Clof_1


title: H3K27me3 OTU5 control rep2

value: otu5 mutant

value: low Pi

tag: tissue


title: H3K27me3 OTU5 control rep1


title: H3K27me3 OTU5 low Pi rep2


title: H3K27me3 OTU5 low Pi rep1


title: S_WT_48HPI_rep3

city: Manhattan

first: Eduard

last: Akhunov

state: Kansas

address: 2245 Buckingham St, Apt 10

department: Plant Pathology

institute: Kansas State University

description:
infected with wild-type Puccnina graminis isolate 99KS76A-1
S_WT_48HPI_rep3

data_processing:
Quality filtering (NGS QC Toolkit v 1.0)
Read alignment using kallisto
Abundance estimation using kallisto
kallisto
Genome_build: TGACv1
Supplementary_files_format_and_content: It is the output file of kallisto. The header is included.

organism: Triticum aestivum

growth_protocol: Plants are grown in growth chamber (16 hour light, 8 hour dark, 21 C) for 2 weeks

extract_protocol:
Trizol extraction from ground tissues
TruSeq RNA Sample Preparation kit v2 (Illumina)

treatment_protocol: Plants were inoculated by spraying with a suspension of Puccinia graminis urediniospores in the isoparaffin solvent Soltrol 170 (Chevron Phillips Chemical, TX). Seedlings were incubated in a dew chamber (20°C) in dark conditions for 12 hours followed by 1 hour incubation under light. Inoculated seedlings were kept in a growth chamber at 22°C with a 16 h / 8 h (day/night) photoperiod.

tag: cultivar

value: Fielder

tag: infected with

value: wild type Puccinia graminis f.sp. tritici (Pgt) isolate 99KS76A-1

value: leaf

tag: time point (hr after inoculation)


title: S_WT_96HPI_rep1

description:
infected with wild-type Puccnina graminis isolate 99KS76A-1
S_WT_96HPI_rep1


title: S_WT_96HPI_rep2

description:
infected with wild-type Puccnina graminis isolate 99KS76A-1
S_WT_96HPI_rep2


title: S_WT_96HPI_rep3

description:
infected with wild-type Puccnina graminis isolate 99KS76A-1
S_WT_96HPI_rep3


title: S_WT_48HPI_rep2

description:
infected with wild-type Puccnina graminis isolate 99KS76A-1
S_WT_48HPI_rep2


title: S_WT_48HPI_rep1

description:
infected with wild-type Puccnina graminis isolate 99KS76A-1
S_WT_48HPI_rep1


title: H3K27me3 WT control rep1

value: wild type


title: H3K27me3 WT control rep2


title: H3K4me3 OTU5 low Pi rep2


title: S_WT_24HPI_rep3

description:
infected with wild-type Puccnina graminis isolate 99KS76A-1
S_WT_24HPI_rep3


title: H3K4me3 OTU5 low Pi rep1


title: S_WT_24HPI_rep2

description:
infected with wild-type Puccnina graminis isolate 99KS76A-1
S_WT_24HPI_rep2


title: v65.h3k27me3

tag: cell line


title: H3K4me3 WT low Pi rep2


title: S_WT_24HPI_rep1

description:
infected with wild-type Puccnina graminis isolate 99KS76A-1
S_WT_24HPI_rep1


title: H3K27me3 WT low Pi rep2


title: H3K4me3 WT low Pi rep1


title: H3K4me3 OTU5 control rep2


title: S_M7_96HPI_rep1

description:
infected with Puccnina graminis mutant M7
S_M7_96HPI_rep1

value: P. graminis f.sp. tritici mutant M7 carrying loss-of-function mutations in the AvrSr35 gene


title: H3K4me3 OTU5 control rep1


title: S_M7_96HPI_rep3

description:
infected with Puccnina graminis mutant M7
S_M7_96HPI_rep3


title: S_M7_96HPI_rep2

description:
infected with Puccnina graminis mutant M7
S_M7_96HPI_rep2


title: S_M7_48HPI_rep3

description:
infected with Puccnina graminis mutant M7
S_M7_48HPI_rep3


title: S_M7_48HPI_rep1

description:
infected with Puccnina graminis mutant M7
S_M7_48HPI_rep1


title: S_M7_48HPI_rep2

description:
infected with Puccnina graminis mutant M7
S_M7_48HPI_rep2


title: S_M7_24HPI_rep3

description:
infected with Puccnina graminis mutant M7
S_M7_24HPI_rep3


title: hek293.h3k4me3


title: H3K4me3 WT control rep1


title: S_M7_24HPI_rep1

description:
infected with Puccnina graminis mutant M7
S_M7_24HPI_rep1


title: S_M7_24HPI_rep2

description:
infected with Puccnina graminis mutant M7
S_M7_24HPI_rep2


title: S_M4_96HPI_rep3

description:
infected with Puccnina graminis mutant M4
S_M4_96HPI_rep3

value: P. graminis f.sp. tritici mutant M4 carrying loss-of-function mutations in the AvrSr35 gene


title: hek293.h3k4me1


title: hek293.h3k27ac


title: hek293.flag.control

value: FLAG


title: hek293.flag.brwd2


title: S_M4_96HPI_rep1

description:
infected with Puccnina graminis mutant M4
S_M4_96HPI_rep1


title: S_M4_48HPI_rep3

description:
infected with Puccnina graminis mutant M4
S_M4_48HPI_rep3


title: dm3.rna.dsLacZ.rep2.exp1

organism: Drosophila melanogaster

source_name: Drosophila S2 cells

value: Drosophila S2 cells

value: lacZ RNAi


title: dm3.rna.dsLacZ.rep2.exp2


title: dm3.rna.dsLacZ.rep1.exp2


title: H3K4me3 WT control rep2


title: hek293.brwd2.833


title: S_M4_48HPI_rep2

description:
infected with Puccnina graminis mutant M4
S_M4_48HPI_rep2


title: hct116.rna.del.brwd2.rep2


title: hek293.input


title: S_M4_48HPI_rep1

description:
infected with Puccnina graminis mutant M4
S_M4_48HPI_rep1


title: hct116.rna


title: hek293.h3k4me2


title: dm3.rna.dsBrwd.rnai.2.exp2

value: dBRWD3 RNAi 2


title: dm3.rna.dsLacZ.rep1.exp1


title: S_M4_24HPI_rep3

description:
infected with Puccnina graminis mutant M4
S_M4_24HPI_rep3


title: hct116.input.mll1.ko.exp2

value: ChIP-Input


title: hct116.input.exp2


title: hct116.rna.del.brwd2.rep1


title: dm3.rna.dsBrwd.rnai.2.exp1


title: S_M4_96HPI_rep2

description:
infected with Puccnina graminis mutant M4
S_M4_96HPI_rep2


title: S_M4_24HPI_rep2

description:
infected with Puccnina graminis mutant M4
S_M4_24HPI_rep2


title: dm3.rna.dsBrwd.rnai.1.exp2

value: dBRWD3 RNAi 1


title: S_M4_24HPI_rep1

description:
infected with Puccnina graminis mutant M4
S_M4_24HPI_rep1


title: hct116.input.del.mll4.set


title: hct116.input.del.brwd2


title: dm3.rna.dsBrwd.rnai.1.exp1


title: hct116.input


title: hct116.h3k4me3.exp2


title: dm3.input.dsBrwd.rnai.2


title: S_M1_96HPI_rep2

description:
infected with Puccnina graminis mutant M1
S_M1_96HPI_rep2

value: P. graminis f.sp. tritici mutant M1 carrying loss-of-function mutations in the AvrSr35 gene


title: S_M1_96HPI_rep3

description:
infected with Puccnina graminis mutant M1
S_M1_96HPI_rep3


title: S_M1_96HPI_rep1

description:
infected with Puccnina graminis mutant M1
S_M1_96HPI_rep1


title: hct116.h3k4me3.del.mll1.ko.exp2


title: S_M1_48HPI_rep1

description:
infected with Puccnina graminis mutant M1
S_M1_48HPI_rep1


title: S_M1_48HPI_rep3

description:
infected with Puccnina graminis mutant M1
S_M1_48HPI_rep3


title: dm3.h3k4me3.dsLacZ.exp1


title: dm3.h3k4me3.dsLacZ.exp2


title: dm3.h3k4me3.dsBrwd.rnai.2.exp1


title: hct116.h3k4me3.del.mll4.set


title: S_M1_48HPI_rep2

description:
infected with Puccnina graminis mutant M1
S_M1_48HPI_rep2


title: S_M1_24HPI_rep3

description:
infected with Puccnina graminis mutant M1
S_M1_24HPI_rep3


title: hct116.h3k4me3


title: dm3.h3k4me3.dsBrwd.rnai.2.exp2


title: dm3.h3k4me3.dsBrwd.rnai.1.exp2


title: hct116.h3k4me2.exp2


title: S_M1_24HPI_rep2

description:
infected with Puccnina graminis mutant M1
S_M1_24HPI_rep2


title: dm3.h3k4me3.dsBrwd.rnai.1.exp1


title: dm3.h3k4me1.dsLacZ.exp2


title: hct116.h3k4me2.del.mll1.ko.exp2


title: hct116.h3k4me2.del.mll4.set


title: dm3.h3k4me1.dsLacZ.exp1


title: dm3.input.dsBrwd.rnai.1


title: S_M1_24HPI_rep1

description:
infected with Puccnina graminis mutant M1
S_M1_24HPI_rep1


title: Mock24H_rep3

description:
mock inoculation
Mock24H_rep3

value: mock; non-infected control


title: Mock24H_rep2

description:
mock inoculation
Mock24H_rep2


title: WGBS WT low Pi rep2

data_processing:
RNA-seq alignment using Tophat 2.0.4, TAIR10 as library junction
Abundance counting using cuffdiff
Calculate RPKM by dividing by union length of exons in kilbases and number of reads mapped in millions, as reported by cuffdiff
BS-seq reads were aligned to the TAIR10 genome using BS Seeker2
If multiple alignments mapped to the same location only one is kept.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data (CGmap) is in text format.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

extract_protocol:
Genomic DNA was isolated from rosette leaves using a Wizard Genomic DNA Purification kit A1120 (Promega, USA). The procedure involves lysis of isolated nuclei, RNase digestion, protein precipitation, centrifugation, precipitation of DNA from the supernatant using isopropanol, followed by a wash step with 70% ethanol. After pelleting the precipitated DNA by centrifugation, it was dried under a vacuum and rehydrated in sterile nuclease free water.
Total RNA was isolated from rosette leaves using a Plant total RNA Purification kit Cat#TR02 (Gene Mark, Taiwan). The procedure involves cell lysis and protein precipitation followed by centrifugation. RNA in the supernatant is then bound on a filter column, where it is digested with DNaseI, followed by washing, and eluting with nuclease-free waster.
BS-seq: Genomic DNA was sheared by sonication to generate DNA fragments in the 100-300 bp size range. Bisulfite treatment and library preparation were carried out as described (Feng et al. 2011), except that the invitrogen methylcode bisulfite conversion kit was utilized for bisulfite treatment. The resulting libraries were sequenced with  Illumina sequencing technology.
RNA-seq: RNA was quantified with the Qubit RNA BR Assay and 10 μg of purified RNA was utilized as starting material for library construction, which was carried out with the Dynabeads for polyA RNA enrichment, Superscript III cDNA synthesis, and barcoded with illumina index.  Libraries were sequenced using 100-bp reads on the Illumina System.

value: root

value: high Pi


title: hct116.h3k4me2


title: Mock24H_rep1

description:
mock inoculation
Mock24H_rep1


title: WGBS OTU5 low Pi rep1

value: otu5 mutant

value: low Pi


title: hct116.h3k4me1.exp2


title: dm3.h3k4me1.dsBrwd.rnai.2.exp1


title: Trichoderma reesei QM9414 Δxyr1Δara1  growth D-galactose replicate 2

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

institute: Centre of fungal biodiversity

description: QM9414 Δxyr1Δara1

data_processing:
Illumina data analysis pipeline RTA v2.4.11 abd Bcl2dastq v2.17 softwares used for basecalling.
Adaptor sequences were removed using Trimmomatic v0.30. Clean reads were mapped to the genome sequence using TopHat mismatch 2%. Reads were map to genes using HTSeq-count.
FPKM values were calculated using Cufflinks with default options
Genome_build: T. reesei QM6a v.2 (http://genome.jgi.doe.gov/Trire2/Trire2.home.html)
Supplementary_files_format_and_content: excel file include gene length, expected count and FPKM for each sample.

organism: Trichoderma reesei

source_name: QM9414 Δxyr1Δara1

growth_protocol: A transfer experiment was performed for transcriptomics. 250 mL of complete medium (CM) (de Vries, et al. Appl Environ Microbiol 2004:70, 3954-9) containing 2% D-fructose in 1 L Erlenmeyer flasks was inoculated with 2.5 x 108 fresh spores, harvested from a PDA plate, and incubated in a rotatory shaker at 28°C for 20 h at 250 rpm. The mycelium was harvested by filtration, washed with liquid Mandels Andreotti medium (MA) (Mandels, M. and Andreotti, R.E. Process Biochemistry 1978:13-6:15) (without carbon source) and 2.5 g mycelium (wet weight) was transferred to 250 mL Erlenmeyer flasks containing 50 mL MA with 25 mM D-galactose or L-arabinose, and incubated in a rotatory shaker at 28°C and 250 rpm.

extract_protocol:
RNA samples (5-41 μg DNase-treated total RNA) were processed by GenomeScan (Leiden, The Netherlands) according to the company's workflow pipeline.
The sample preparation was performed according to the protocol “NEBNext Ultra Directional RNA Library Prep Kit for Illumina”.

treatment_protocol: After 2 h of incubation, the mycelium was harvested by vacuum filtration, dried between tissue paper, directly frozen in liquid nitrogen and stored at -45°C.

value: QM9414 delta xyr1delta ara1

tag: substrate

value: MM + 25 mM D-galactose

tag: sampling time

value: 2 hours


title: WGBS WT low Pi rep1

value: wild type


title: hct116.h3k4me1.del.mll4.set


title: dm3.h3k4me1.dsBrwd.rnai.1.exp2


title: WGBS OTU5 control rep2


title: dm3.h3k4me1.dsBrwd.rnai.1.exp1


title: hct116.h3k4me1.del.mll1.ko.exp2


title: hct116.h3k4me1.del.brwd2


title: WGBS OTU5 low Pi rep2


title: Trichoderma reesei QM9414 Δxyr1Δara1  growth D-galactose replicate 1

description: QM9414 Δxyr1Δara1


title: dm3.h3k27ac.dsLacZ.exp2


title: WGBS WT control rep2


title: Trichoderma reesei QM9414 Δara1  growth D-galactose replicate 2

description: QM9414 Δara1

source_name: QM9414 Δara1

value: QM9414 delta ara1


title: WGBS OTU5 control rep1


title: Trichoderma reesei QM9414 Δara1  growth D-galactose replicate 1

description: QM9414 Δara1


title: hct116.h3k4me1


title: Trichoderma reesei QM9414 Δxyr1  growth D-galactose replicate 2

description: QM9414 Δxyr1

source_name: QM9414 Δxyr1

value: QM9414 delta xyr1


title: hct116.brwd2.del.mll1.ko.exp2

value: BRWD2 833


title: dm3.h3k4me1.dsBrwd.rnai.2.exp2

value: Drosophila S2 cells


title: WGBS WT control rep1


title: dm3.h3k27ac.dsBrwd.rnai.2.exp2

value: dBRWD3 RNAi 2


title: hct116.brwd2.834.del.mll4.set


title: RNA OTU5 low Pi rep3

description: processed data file: rpkm_table.txt


title: hct116.brwd2.834.del.brwd2


title: RNA OTU5 low Pi rep2

description: processed data file: rpkm_table.txt


title: Trichoderma reesei QM9414 Δxyr1  growth D-galactose replicate 1

description: QM9414 Δxyr1


title: Trichoderma reesei QM9414  growth D-galactose replicate 2

source_name: QM9414 wild type, ATCC 26921


title: dm3.h3k27ac.dsBrwd.rnai.2.exp1


title: dm3.h3k27ac.dsBrwd.rnai.1.exp2


title: RNA OTU5 low Pi rep1

description: processed data file: rpkm_table.txt


title: RNA WT low Pi rep3

description: processed data file: rpkm_table.txt


title: dm3.h3k27ac.dsBrwd.rnai.1.exp1


title: hct116.brwd2.833.exp2


title: dm3.h3k27ac.dsLacZ.exp1

value: lacZ RNAi


title: Trichoderma reesei QM9414 Δxyr1Δara1  growth L-arabinose replicate 2

description: QM9414 Δxyr1Δara1

value: MM + 25 mM L-arabinose


title: Trichoderma reesei QM9414  growth D-galactose replicate 1


title: hct116.brwd2.833.del.brwd2


title: RNA WT low Pi rep2

description: processed data file: rpkm_table.txt


title: RNA OTU5 control rep3

description: processed data file: rpkm_table.txt


title: Trichoderma reesei QM9414 Δara1  growth L-arabinose replicate 1

description: QM9414 Δara1


title: dm3.dsLacZ.input


title: hct116.brwd2.833.del.mll4.set


title: dm3.brwd


title: RNA WT low Pi rep1

description: processed data file: rpkm_table.txt


title: hct116.brwd2.833


title: WT_15

city: Dundee

first: Shuyu

last: Li

address: Dow Street

institute: University of Dundee

data_processing:
Reads were mapped to S. cerevisiae (Ensemble R64) genome using BWA
Wig files were created from BAM files, using own software
Genome_build: Ensemble R64

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast cells were treated with a factor for 2.5 hrs, subsequently release and re-arrested in metaphase for 2.5 hrs. Equal volume cells was collected at 0, 10 and 15minutes after release to anaphase.

extract_protocol: For crosslinking, cells were incubated with 1% formaldehyde overnight at 4°C. Cells were harvested and washed three times with ice-cold TBS, and cells were transferred to 1.5 ml tube. For cell breakage, 300 ml of lysis buffer and glass beads were added to the tube, and placed tubes into the cells disruptor (FastPrep-24 5G), and disrupt cell wall at speed 6.0 m/sec for 40 sec, repeat the disruption procedure once more to achieve better results. The cell lysate was sonicated with Bioruptor (Diagenode, 30sec ´ 30 cycles with 30 sec intervals with high intensity), resulting in an average fragment size of 300~200 bp. The lysate was clarified by centrifugation at 13,000 rpm for 5 minutes. For immunoprecipitation, 60 ml of magnetic beads (Dynabeads Pan Mouse IgG, Invitrogen) were added following pre-incubatition with an anti-HA monoclonal antibody (HA.11, Covance).

treatment_protocol: SMC1 was tagged with HA, and anti-HA antibody was used for immunoprecipitation

tag: genotype


title: Trichoderma reesei QM9414 Δara1  growth L-arabinose replicate 2

description: QM9414 Δara1


title: hos1_aid_15

value: Hos1 depletion


title: Trichoderma reesei QM9414 Δxyr1  growth L-arabinose replicate 2

description: QM9414 Δxyr1


title: hct116.brwd2.834


title: Trichoderma reesei QM9414 Δxyr1  growth L-arabinose replicate 1

description: QM9414 Δxyr1


title: Trichoderma reesei QM9414 Δxyr1Δara1  growth L-arabinose replicate 1

description: QM9414 Δxyr1Δara1


title: RNA WT control rep2

description: processed data file: rpkm_table.txt


title: hos1_aid_0


title: RNA WT control rep3

description: processed data file: rpkm_table.txt


title: hos1_aid_10


title: NAF+LO(22RV1)-2

city: Los Angeles

first: Sungyong

last: You

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

data_processing:
Raw reads obtained from RNA-Seq were aligned to the custom human GRCh38 transcriptome reference (http://www.gencodegenes.org) using Bowtie (version 1.1.1)65 and RSEM (version 1.2.20)66 with default parameters.
Expression counts for each gene, fragments per kilobase of transcript per million (FPKM), in all samples were normalized by the sequencing depth.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM

source_name: normal associated human prostatic fibroblasts treated with large oncosomes

growth_protocol: fibroblasts  were maintained in culture in 10% FBS supplemented DMEM medium

extract_protocol:
samples were collected in Trizol and total RNA was extracted using the RNeasy Mini Kit (Qiagen). RNA concentration and quality were tested respectively with Nanodrop 8000 (Thermo Scientific) and 2100 Bioanalyzer (Agilent)
1 μg of total RNA per sample was used for library construction with the Illumina TruSeq stranded mRNA library preparation kit. Briefly streptavidin-coated magnetic beads were employed for poly-A mRNA selection and cDNA was synthesized from enriched and fragmented RNA using reverse transcriptase (Super-Script II, Invitrogen) and random primers. After conversion into double stranded DNA and PCR amplification the products were enriched for library preparation and purified using Agencourt AMPure XP beads (Beckman Coulter Genomics).

treatment_protocol: serum starved fibroblasts were exposed for 6h to vehiclle or 20ug/ml of cancer cell derived large oncosomes

value: fibroblasts from surgical explants of patients diagnosed with benign prostatic hyperplasia

value: prostate


title: NAF+LO(22RV1)-1


title: Trichoderma reesei QM9414  growth L-arabinose replicate 1


title: Trichoderma reesei QM9414  growth L-arabinose replicate 2


title: RNA OTU5 control rep1

description: processed data file: rpkm_table.txt

value: root


title: NAF control-1

source_name: normal associated human prostatic fibroblasts


title: NAF control-2


title: WT_10


title: RNA WT control rep1

description: processed data file: rpkm_table.txt

data_processing:
RNA-seq alignment using Tophat 2.0.4, TAIR10 as library junction
Abundance counting using cuffdiff
Calculate RPKM by dividing by union length of exons in kilbases and number of reads mapped in millions, as reported by cuffdiff

BS-seq reads were aligned to the TAIR10 genome using BS Seeker2
If multiple alignments mapped to the same location only one is kept.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data (CGmap) is in text format.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

value: high Pi


title: RNA OTU5 control rep2

description: processed data file: rpkm_table.txt

value: otu5 mutant

value: low Pi


title: GBM cell 1505

status: Public on Nov 01 2017

city: Stanford

first: Spyros

last: Darmanis

state: California

address: Clark Center, E300

department: Bioengineering

institute: Stanford University

description:
Single cell from Tumor
1001000033.H5

data_processing:
Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65).  We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore  (--stringency 1).
Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ).
Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

source_name: Brain

extract_protocol:
single-cell sorting in 96-well plates followed by cDNA preparation using Smart-seq2
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT. Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2

tag: diagnosis

value: glioblastoma

tag: plate id

tag: well

value: Tumor

tag: patient id

tag: tsne cluster

value: Immune cell

tag: neoplastic

value: Regular

tag: selection


title: GBM cell 1503

description:
Single cell from Tumor
1001000033.H7

tag: cell type


title: GBM cell 1501

description:
Single cell from Tumor
1001000033.H3


title: GBM cell 1497

description:
Single cell from Tumor
1001000033.H10


title: GBM cell 1502

description:
Single cell from Tumor
1001000033.D6


title: GBM cell 1499

description:
Single cell from Tumor
1001000033.F12

value: Neoplastic


title: GBM cell 1500

description:
Single cell from Tumor
1001000033.A12


title: GBM cell 1493

description:
Single cell from Tumor
1001000033.G9


title: GBM cell 1504

description:
Single cell from Tumor
1001000033.E9


title: GBM cell 1498

description:
Single cell from Tumor
1001000033.G12


title: GBM cell 1495

description:
Single cell from Tumor
1001000033.F9


title: GBM cell 1496

description:
Single cell from Tumor
1001000033.F10


title: GBM cell 1506

description:
Single cell from Tumor
1001000033.H4


title: GBM cell 1492

description:
Single cell from Tumor
1001000033.G1


title: GBM cell 1494

description:
Single cell from Tumor
1001000033.B2


title: GBM cell 1491

description:
Single cell from Tumor
1001000033.H2


title: GBM cell 1489

description:
Single cell from Tumor
1001000033.C7


title: WT_0

value: wild type


title: GBM cell 1490

description:
Single cell from Tumor
1001000033.C11


title: GBM cell 1488

description:
Single cell from Tumor
1001000033.E2


title: GBM cell 1487

description:
Single cell from Tumor
1001000033.D8


title: GBM cell 1485

description:
Single cell from Tumor
1001000033.B3


title: GBM cell 1483

description:
Single cell from Tumor
1001000033.C5


title: GBM cell 1482

description:
Single cell from Tumor
1001000033.D9


title: GBM cell 1481

description:
Single cell from Tumor
1001000033.A7


title: GBM cell 1484

description:
Single cell from Tumor
1001000033.B5


title: GBM cell 1480

description:
Single cell from Tumor
1001000033.E6


title: GBM cell 1479

description:
Single cell from Tumor
1001000033.F11


title: GBM cell 1478

description:
Single cell from Tumor
1001000033.A4


title: GBM cell 1475

description:
Single cell from Tumor
1001000033.A6


title: GBM cell 1471

description:
Single cell from Tumor
1001000033.F6


title: GBM cell 1486

description:
Single cell from Tumor
1001000033.G11


title: GBM cell 1463

description:
Single cell from Tumor
1001000033.B11


title: GBM cell 1462

description:
Single cell from Tumor
1001000032.E7

value: Vascular

value: Endothelial(BSC)


title: GBM cell 1461

description:
Single cell from Tumor
1001000032.B2


title: GBM cell 1465

description:
Single cell from Tumor
1001000033.A5


title: GBM cell 1468

description:
Single cell from Tumor
1001000033.E4


title: GBM cell 1464

description:
Single cell from Tumor
1001000033.A11


title: GBM cell 1474

description:
Single cell from Tumor
1001000033.E5


title: GBM cell 1466

description:
Single cell from Tumor
1001000033.F3


title: GBM cell 1476

description:
Single cell from Tumor
1001000033.C10


title: GBM cell 1472

description:
Single cell from Tumor
1001000033.E8


title: GBM cell 1454

description:
Single cell from Tumor
1001000032.D10


title: GBM cell 1453

description:
Single cell from Tumor
1001000032.G10


title: GBM cell 1456

description:
Single cell from Tumor
1001000032.G4


title: GBM cell 1469

description:
Single cell from Tumor
1001000033.B12


title: GBM cell 1459

description:
Single cell from Tumor
1001000032.F10


title: GBM cell 1452

description:
Single cell from Tumor
1001000032.C3


title: GBM cell 1473

description:
Single cell from Tumor
1001000033.C12


title: GBM cell 1451

description:
Single cell from Tumor
1001000032.C7


title: GBM cell 1457

description:
Single cell from Tumor
1001000032.B7


title: GBM cell 1460

description:
Single cell from Tumor
1001000032.E5


title: GBM cell 1455

description:
Single cell from Tumor
1001000032.H5


title: GBM cell 1467

description:
Single cell from Tumor
1001000033.D12


title: GBM cell 1449

description:
Single cell from Tumor
1001000032.F12


title: GBM cell 1470

description:
Single cell from Tumor
1001000033.E10


title: GBM cell 1450

description:
Single cell from Tumor
1001000032.A12


title: GBM cell 1477

description:
Single cell from Tumor
1001000033.F7


title: GBM cell 1458

description:
Single cell from Tumor
1001000032.C11


title: GBM cell 1448

description:
Single cell from Tumor
1001000032.D9


title: GBM cell 1446

description:
Single cell from Tumor
1001000032.C8


title: GBM cell 1443

description:
Single cell from Tumor
1001000032.F9


title: GBM cell 1445

description:
Single cell from Tumor
1001000032.B12


title: GBM cell 1439

description:
Single cell from Tumor
1001000032.G11


title: GBM cell 1442

description:
Single cell from Tumor
1001000032.D11


title: GBM cell 1447

description:
Single cell from Tumor
1001000032.B6


title: GBM cell 1438

description:
Single cell from Tumor
1001000032.F5


title: GBM cell 1441

description:
Single cell from Tumor
1001000032.F6


title: GBM cell 1433

description:
Single cell from Tumor
1001000032.A9


title: GBM cell 1440

description:
Single cell from Tumor
1001000032.B8


title: GBM cell 1431

description:
Single cell from Tumor
1001000032.E2


title: GBM cell 1430

description:
Single cell from Tumor
1001000032.F11


title: GBM cell 1437

description:
Single cell from Tumor
1001000032.B9


title: GBM cell 1427

description:
Single cell from Tumor
1001000032.C10


title: GBM cell 1429

description:
Single cell from Tumor
1001000032.F1


title: GBM cell 1425

description:
Single cell from Tumor
1001000032.H10


title: GBM cell 1426

description:
Single cell from Tumor
1001000032.A10


title: GBM cell 1436

description:
Single cell from Tumor
1001000032.E10


title: GBM cell 1435

description:
Single cell from Tumor
1001000032.D12


title: GBM cell 1422

description:
Single cell from Tumor
1001000032.F8


title: GBM cell 1423

description:
Single cell from Tumor
1001000032.E9


title: GBM cell 1428

description:
Single cell from Tumor
1001000032.A5


title: GBM cell 1432

description:
Single cell from Tumor
1001000032.B5


title: GBM cell 1417

description:
Single cell from Tumor
1001000031.H9


title: GBM cell 1420

description:
Single cell from Tumor
1001000032.D8


title: GBM cell 1434

description:
Single cell from Tumor
1001000032.D6


title: GBM cell 1421

description:
Single cell from Tumor
1001000032.D2


title: GBM cell 1411

description:
Single cell from Tumor
1001000031.H4


title: GBM cell 1418

description:
Single cell from Tumor
1001000032.F7


title: GBM cell 1412

description:
Single cell from Tumor
1001000031.D12


title: GBM cell 1444

description:
Single cell from Tumor
1001000032.G8


title: GBM cell 1424

description:
Single cell from Tumor
1001000032.G12


title: GBM cell 1419

description:
Single cell from Tumor
1001000032.C4


title: GBM cell 1415

description:
Single cell from Tumor
1001000031.H1


title: GBM cell 1404

description:
Single cell from Tumor
1001000031.F9


title: GBM cell 1408

description:
Single cell from Tumor
1001000031.E4

value: OPC


title: GBM cell 1414

description:
Single cell from Tumor
1001000031.F4


title: GBM cell 1401

description:
Single cell from Tumor
1001000031.E1


title: GBM cell 1413

description:
Single cell from Tumor
1001000031.E6


title: GBM cell 1409

description:
Single cell from Tumor
1001000031.B12


title: GBM cell 1407

description:
Single cell from Tumor
1001000031.A3


title: GBM cell 1406

description:
Single cell from Tumor
1001000031.F3


title: GBM cell 1405

description:
Single cell from Tumor
1001000031.A5


title: GBM cell 1399

description:
Single cell from Tumor
1001000031.G10


title: GBM cell 1398

description:
Single cell from Tumor
1001000031.C2


title: GBM cell 1403

description:
Single cell from Tumor
1001000031.C1


title: GBM cell 1395

description:
Single cell from Tumor
1001000031.F7


title: GBM cell 1402

description:
Single cell from Tumor
1001000031.A7


title: GBM cell 1394

description:
Single cell from Tumor
1001000031.H10


title: GBM cell 1396

description:
Single cell from Tumor
1001000031.G1


title: GBM cell 1410

description:
Single cell from Tumor
1001000031.A4


title: GBM cell 1416

description:
Single cell from Tumor
1001000031.G5


title: GBM cell 1393

description:
Single cell from Tumor
1001000031.B9


title: GBM cell 1392

description:
Single cell from Tumor
1001000031.C10


title: GBM cell 1391

description:
Single cell from Tumor
1001000031.A9


title: GBM cell 1390

description:
Single cell from Tumor
1001000031.C11


title: GBM cell 1389

description:
Single cell from Tumor
1001000031.E12


title: GBM cell 1388

description:
Single cell from Tumor
1001000031.E5


title: GBM cell 1387

description:
Single cell from Tumor
1001000031.E2


title: GBM cell 1386

description:
Single cell from Tumor
1001000031.G12


title: GBM cell 1384

description:
Single cell from Tumor
1001000031.A2


title: GBM cell 1385

description:
Single cell from Tumor
1001000031.F1


title: GBM cell 1380

description:
Single cell from Tumor
1001000031.H7


title: GBM cell 1382

description:
Single cell from Tumor
1001000031.G7


title: GBM cell 1400

description:
Single cell from Tumor
1001000031.A10


title: GBM cell 1379

description:
Single cell from Tumor
1001000031.C7