title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 7

source_name: cell line SCC25,cetuximab,week 7

value: CTX generation 7 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with PBS, week 10

status: Public on Apr 24 2018

type: genomic

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

country: USA

institute: University of Maryland, Baltimore

hyb_protocol: Samples were loaded to the Beadchip and incubated in the Illumina Hybridization Oven, according to manufacturer's protocol

scan_protocol: Beadchips were scanned using the Methylation Module of GenomeStudio 1.0 of the Illumina HiScan equiptment.

data_processing: iDat files were loaded with minfi version 1.16.1 and used to compute beta values for each probe.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line SCC25,PBS,week 10

label_protocol: Infinium Human MethylationEPIC Beadchip Kit (Illumina), following manufacturer's instructions.

extract_protocol: Dneasy Blood & Tissue Kit following manufacturer's instructions.

tag: sample type

value: PBS generation 10 for SCC25 cetuximab resistant generations

tag: generations

tag: treatment

value: PBS

tag: cetuximab resistant clone

tag: batch


title: HNSCC sensitive cell line SCC25 treated with PBS, week 11

source_name: cell line SCC25,PBS,week 11

value: PBS generation 11 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with PBS, week 8

source_name: cell line SCC25,PBS,week 8

value: PBS generation 8 for SCC25 cetuximab resistant generations


title: Cetuximab resistant clones derived from SCC25, CTXR4

source_name: SCC25 clone, PBS, CTXR4

value: SCC25 cetuximab resistant clone 4


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 8

source_name: cell line SCC25,cetuximab,week 8

value: CTX generation 8 for SCC25 cetuximab resistant generations

value: 100nM Cetuximab


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 9

source_name: cell line SCC25,cetuximab,week 9

value: CTX generation 9 for SCC25 cetuximab resistant generations


title: 82Q Rep 2

type: SRA

city: Minneapolis

first: Christine

middle: M.

last: Henzler

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Twin Cities (Minneapolis, MN, US)

library_source: transcriptomic

data_processing:
Illumina HiSeq 2000 software used for basecalling
Raw reads were first groomed by trimming the first 12bpfrom the 5'-ends with random base concentration, then mapped to UCSC mm10 using STAR aligner (STAR-2.5.3a)
Expression level for each gene was estimated using Python program HTSeq (Anders et al., Bioinformatics 2014). Specifically htseq-count function of HTSeq accumulated the number of aligned reads that falls under
Using the obtained read counts, differential gene analyses were carried out using the DESeq2 package in the R environment.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Text files inclue read counts value for each gene; individual file for each sample.

molecule: total RNA

organism: Mus musculus

source_name: Brain cerebellar tissue

growth_protocol: standard animal house conditions

extract_protocol:
Mice were euthanized under anesthesia and cerebella were quickly dissected over ice. RNA was extracted following published protocols. Isolated RNA was submitted to the University of Minnesota Genomics Center. Sample quality checks using the NanoDrop spectrophotometer and Agilent Bioanalyzer 2100 were conducted.
Using NuGEN Ovation RNA-Seq System v2, purified double-stranded cDNA was generated from 10 ng of total RNA and amplified using both 3’ poly (A) selection and random priming. 2 µg of each sample was sheared using the Covaris S2 focused-ultrasonicator following the manufacturer’s protocol to obtain a final library with insert size of 400 bp. The sheared samples were quantified using the NanoDrop ND-1000 spectrophotometer and Invitrogen Qubit 2.0 DNA quantitation assay. The fragment sizes were confirmed on the Agilent Bioanalyzer to verify proper shearing. A double-stranded DNA library was produced using Illumina TruSeq DNA library preparation system and the sequencing was run on a HiSeq 2500 system.

tag: strain

value: FVB

tag: tissue

value: Cerebellum

tag: genotype


title: HNSCC sensitive cell line SCC25 treated with PBS, week 7

source_name: cell line SCC25,PBS,week 7

value: PBS generation 7 for SCC25 cetuximab resistant generations


title: 591 Rep 5


title: CicKO Rep4

value: En1-Cre; Cicflox/flox


title: Wildtype Rep3

value: Cicflox/+


title: HNSCC sensitive cell line SCC25 treated with PBS, week 6

source_name: cell line SCC25,PBS,week 6

value: PBS generation 6 for SCC25 cetuximab resistant generations


title: 591 Rep 3


title: 591 Rep 4


title: HNSCC sensitive cell line SCC25 treated with PBS, week 5

source_name: cell line SCC25,PBS,week 5

value: PBS generation 5 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 4

source_name: cell line SCC25,cetuximab,week 4

value: CTX generation 4 for SCC25 cetuximab resistant generations


title: pondKOV2_larval tail tip_17°C_r3

type: RNA

city: Ploen

first: Till

last: Czypionka

address: August-Thienemann-Strasse 2

department: Evolutionary Genetics

country: Germany

institute: MPI for Evolutionary Biology

hyb_protocol: Labeled cRNA hybridized to the microarrays following Agilent’s ‘One-Color Microarray-Based Gene Expression Analysis protocol’ (version 6.5, May 2010).

scan_protocol: Microarrays were scanned with an Agilent DNA Microarray Scanner type C.

data_processing: Raw signals (gprocessed signal) were extracted using the Agilent Feature Extraction software (version 10.7.3.1). Signals flagged for bad quality or saturated intensity were treated as missing data. Surface bound oligonucleotide probes on microarrays vary widely in their target binding behavior (Pozhitkov et al. 2014), which distorts the relationship between target cRNA concentration and fluorescent signal intensity. Binding behaviour of all probes on the microarray to their specific target transcripts had therefore previously been quantified in calibration experiments (Czypionka et al. (2015) Ecological transcriptomics – a non-lethal sampling approach for endangered fire salamanders. Methods in Ecology & Evolution.; Goedbloed et al. (2017) Parallel habitat acclimatization is realized by the expression of different genes in two closely related salamander species (genus Salamandra). Heredity.). Raw-signal data was normalized for probe-binding behavior as described by Czypionka et al. (2015). Normalized expression values from replicated probes were merged by taking their median and between array normalization was carried out by dividing normalized signal intensities of each array by their 75 percentile.

organism: Salamandra salamandra

source_name: larval tail tip - 17°C

label_protocol: Labelled cRNA was generated using the Agilent Low Input Quick Amp Labelling kit. Single color labeling with Cy3 was performed.

extract_protocol: Total RNA was extracted from tail tips of the salamander larvae using a Trizol protocol.

treatment_protocol: Larvae sampled in the field were first acclimatized to laboratory conditions (temperature: 9°C, food: live chironomid larvae ad libitum, photoperiod adjusted to 14.5 h of daylight simulating spring conditions in nature) for a period of 14 days in tanks filled to a water level of 6 cm. Following acclimatization, larvae were transferred to a custom-made flow through aquarium consisting of four interconnected chambers (volume 27.6 l each) which was set up in a temperature controlled (9°C) room. Water with a temperature of 9°C entered the system at the right chamber at a flow rate of 300 ml/min and left the system at the leftmost chamber. Water temperature in the two chambers at the right remained at a temperature of 9°C (± 0.1°C), but was increased to 17° C (± 0.1°C) with electric aquarium heaters controlled by thermostats in the two chambers on the left. These high and low treatments (9°C and 17°C) were chosen to represent temperatures encountered by salamander larvae in nature. Bubbles from air stones were used to oxygenize and constantly mix the water column within each chamber. Cup cages were constructed from single-use plastic cups the base of which (area 24 cm²) was cut off and replaced with a gauze, thereby allowing water exchange with the treatment chambers. Cup cages were placed in polystyrene floating racks holding up to 20 cages per chamber. Single salamander larvae were transferred randomly to individual cup-cages to avoid artefacts due to direct interaction or spatial clustering. During the 14 days of the experiment, larvae were fed ad libitum with chironomid larvae four times daily. Cup cages were cleaned daily from faeces and dead food items. Water flow rate and temperatures were controlled on a daily basis. At the end of the experiment, larvae were anaesthetized in mildly carbonized water and subsequently killed by kinetic shock. Dead larvae were preserved in RNAlater and stored at -20°C until RNA extraction.

tag: ecotype

value: pond

tag: temperature

tag: source population

value: larval tail tip


title: HNSCC sensitive cell line SCC25 treated with PBS, week 4

source_name: cell line SCC25,PBS,week 4

value: PBS generation 4 for SCC25 cetuximab resistant generations

value: PBS


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 5

source_name: cell line SCC25,cetuximab,week 5

value: CTX generation 5 for SCC25 cetuximab resistant generations


title: pondKOV2_larval tail tip_17°C_r1


title: pondKOV2_larval tail tip_9°C_r4

source_name: larval tail tip - 9°C


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 3

source_name: cell line SCC25,cetuximab,week 3

value: CTX generation 3 for SCC25 cetuximab resistant generations


title: Wildtype Rep1


title: streamKOGC_larval tail tip_17°C_r4

value: stream

value: KOGC


title: 591 Rep 2


title: streamKOGC_larval tail tip_17°C_r5


title: pondKOV2_larval tail tip_9°C_r3


title: pondKOV2_larval tail tip_9°C_r2


title: CicKO Rep3


title: streamKOGC_larval tail tip_17°C_r6


title: streamKOGC_larval tail tip_17°C_r3


title: HNSCC sensitive cell line SCC25 treated with PBS, week 3

source_name: cell line SCC25,PBS,week 3

value: PBS generation 3 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 6

source_name: cell line SCC25,cetuximab,week 6

value: CTX generation 6 for SCC25 cetuximab resistant generations

value: 100nM Cetuximab


title: 591 Rep 1

value: FVB

value: Cerebellum


title: streamKOGC_larval tail tip_17°C_r2


title: CicKO Rep1

value: En1-Cre; Cicflox/flox


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 2

source_name: cell line SCC25,cetuximab,week 2

value: CTX generation 2 for SCC25 cetuximab resistant generations


title: streamKOGC_larval tail tip_17°C_r1


title: pondKOV2_larval tail tip_17°C_r2


title: HNSCC sensitive cell line SCC25 treated with100nM cetuximab, week 1

source_name: cell line SCC25,cetuximab,week 1

value: CTX generation 1 for SCC25 cetuximab resistant generations


title: streamKOGC_larval tail tip_9°C_r6


title: HNSCC sensitive cell line SCC25 treated with PBS, week 2

source_name: cell line SCC25,PBS,week 2

value: PBS generation 2 for SCC25 cetuximab resistant generations


title: CicKO Rep2


title: Wildtype Rep2

value: Cicflox/+


title: pondKOV2_larval tail tip_9°C_r1

value: pond

value: larval tail tip


title: streamKOGC_larval tail tip_9°C_r4


title: streamKOGC_larval tail tip_9°C_r2


title: streamKOGC_larval tail tip_9°C_r1


title: pondKOE_larval tail tip_17°C_r6

value: KOE


title: streamKOGC_larval tail tip_9°C_r3


title: pondKOE_larval tail tip_17°C_r5


title: pondKOE_larval tail tip_17°C_r4


title: HNSCC sensitive cell line SCC25, baseline for cetuximab resistant generations

source_name: cell line SCC25, parental cell line, baseline for generations

value: Baseline for SCC25 cetuximab resistant generations


title: streamKOGC_larval tail tip_9°C_r5


title: CRC grown in fatty liver, Anti-VEGF treated, biological rep1

city: Shanghai

first: Yunlong

last: Yang

address: Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Dong'an road 130

country: China

institute: Fudan University

description: CRC fatty liver AAD 1

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing:
Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.28061

label: biotin

source_name: mouse CRC grown in fatty liver with Anti-VEGF treatment

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix  WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's insTotal RNA was extracted using Takara RNAiso Plus Kit (Cat#9109, Takara, DaLian, LiaoNing, CN)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)tructions.

value: colorectal cancer (CRC)

tag: tumor growth condition

value: in fatty liver

tag: treated with

value: Anti-VEGF


title: CRC grown in fatty liver, Anti-VEGF treated, biological rep2

description: CRC fatty liver AAD 2


title: CRC grown in fatty liver, Anti-VEGF treated, biological rep3

description: CRC fatty liver AAD 3


title: CRC grown in fatty liver, Vehicle treated, biological rep2

description: CRC fatty liver Vehicle 2

source_name: mouse CRC grown in fatty liver with Vehicle treatment

value: vehicle


title: pondKOV2_larval tail tip_17°C_r4


title: pondKOE_larval tail tip_17°C_r1


title: pondKOE_larval tail tip_17°C_r2


title: pondKOE_larval tail tip_9°C_r6


title: HNSCC sensitive cell line SCC25 treated with PBS, week 1

source_name: cell line SCC25,PBS,week 1

value: PBS generation 1 for SCC25 cetuximab resistant generations

value: PBS


title: CRC grown in healthy liver, Anti-VEGF treated, biological rep3

description: CRC healthy liver AAD 3

source_name: mouse CRC grown in healthy liver with Anti-VEGF treatment

value: in healthy liver


title: CRC grown in fatty liver, Vehicle treated, biological rep1

description: CRC fatty liver Vehicle 1


title: CRC grown in healthy liver, Anti-VEGF treated, biological rep2

description: CRC healthy liver AAD 2


title: pondKOE_larval tail tip_9°C_r5


title: pondKOE_larval tail tip_9°C_r4


title: CRC grown in healthy liver, Anti-VEGF treated, biological rep1

description: CRC healthy liver AAD 1


title: pondKOE_larval tail tip_9°C_r3


title: CRC grown in healthy liver, Vehicle treated, biological rep2

description: CRC healthy liver Vehicle 2

source_name: mouse CRC grown in healthy liver with Vehicle treatment


title: pondKOE_larval tail tip_9°C_r2


title: pondKOE_larval tail tip_9°C_r1


title: WT_3D_3_1

first: Yuli

last: Lin

address: No.130, Dong'an Road, Xuhui

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke, then mapped to reference whole genome using bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
Mapped reads were count using RSEM v1.2.12, and Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: colon tissue

growth_protocol: 6-8week BALB/c mice

extract_protocol:
The proximal part of the intestine was collected and washed with ice-cold PBS with syringes. The luminal side of the intestine was scraped by a Cell Scraper to remove luminal content and mucus. The colon was cut into 2 mm pieces and further washed with cold PBS with gentle vortexing, total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: feed 3% DSS ad libitum for 3 days

value: BALB/c

value: colon

value: WT


title: CRC grown in healthy liver, Vehicle treated, biological rep3

description: CRC healthy liver Vehicle 3


title: pondKOE_larval tail tip_17°C_r3

source_name: larval tail tip - 17°C


title: CRC grown in white adipose tissue, biological rep3

description: CRC WAT 3

data_processing:
Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MoGene-2_0-st
program-name = Expression Console
program-version = 1.4.1.46

source_name: mouse CRC grown in white adipose tissue

value: white adipose tissue


title: CRC grown in healthy liver, Vehicle treated, biological rep1

description: CRC healthy liver Vehicle 1


title: CRC grown in fatty liver, Vehicle treated, biological rep3

description: CRC fatty liver Vehicle 3


title: WT_3D_2_1


title: WT_3D_1_1


title: STAT6_3D_3_1


title: CRC grown in white adipose tissue, biological rep2

description: CRC WAT 2


title: STAT6_3D_2_1


title: CRC grown in white adipose tissue, biological rep1

description: CRC WAT 1


title: UC6_d17_MC

city: Amsterdam

first: Fleur

last: Peters

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC (AMC)

hyb_protocol: Isolated genomic DNA (500 ng) was treated with sodium bisulphite using the EZ-96 DNA methylation kit (Zymo Research, Irvine, CA, USA). Hybridization was performed following manufacturer’s instructions. DNA methylation of CpGs was measured by the Illumina HumanMethylation450K BeadChip using the manufacturer’s protocol (Illumina, Inc., San Diego, CA, USA)

scan_protocol: Array was scanned using the iScan beadchip scanner according to Illumina protocol.

data_processing: All data pre-processing and statistical analysis were performed in R software version 3.4.4. Raw methylation data was normalized with lumi (Bioconductor R) to account for differences between the type I and type II intensities.

label: cy3 and cy5

source_name: ucMSC

label_protocol: Standard Infinium Methylation array protocol

growth_protocol: ucMSC were cultured in minimum essential medium Eagle alpha modification (MEM-α; Sigma-Aldrich, St Louis, MO, USA) containing 2 mM L-glutamine (Lonza, Verviers, Belgium), 1% penicillin/streptomycin solution (P/S; 100IU/ml penicillin, 100IU/ml streptomycin; Lonza) and supplemented with 15% batch tested fetal bovine serum (FBS; Lonza) and 1 ng/ml basic fibroblast growth factor (bFGF) (Sigma) and kept at 37C, 5% CO2 and 20% O2. Once a week medium was refreshed and ucMSC were passaged using 0.05% trypsin-EDTA (Life technologies, Paisley, UK) at ~80-90% confluence. All ucMSC used in experiments were between passage 3-6.

extract_protocol: Genomic DNA was extracted using a Qiagen QIAamp Micro kit according to the manufacturers protocol.

treatment_protocol: Priming of ucMSC  ucMSC of 4 different umbilical cord donors were stimulated with factors were known to modify MSC function or phenotype, as demonstrated in previous studies [10, 32]. At day 0, MSC (confluent culture) were stimulated for three days with interferon gamma (IFNγ, 50 ng/ml; Life technologies, transforming growth factor beta 1 (TGFβ, 10ng/ml; R&D systems, MN, USA) or a multi-factor combination (MC) of IFNγ, TGFβ and retinoic acid (RA, 100 μM; Sigma). At day 3, cells were trypsinised and either used for experiment or snap frozen in pellets containing 300,000 cells and stored at -80°C.   Culture expansion of MSC  At day 0, MSC of 4 different umbilical cord donors were seeded (250,000 cells/T175 flask). Medium was partly refreshed (50%) every 5/6 days. At day 14, cells were used for experiment or snap frozen as pellets for future use.

tag: tissue of origin

value: umbilical cord

tag: donor

tag: time point

value: day 17

value: Multi-factor combination stimulated


title: CRC grown in non-adipose tissue, biological rep2

description: CRC non-adipose 2

source_name: mouse CRC grown in non-adipose tissue

value: non-adipose tissue


title: STAT6_3D_1_1


title: UC7_d17_MC


title: UC12_d17_MC


title: UC2_d17_TGFb

value: TGF-beta stimulated


title: CRC grown in non-adipose tissue, biological rep3

description: CRC non-adipose 3


title: CRC grown in non-adipose tissue, biological rep1

description: CRC non-adipose 1


title: UC12_d17_TGFb


title: HCMV infected Kasumi-3 cells, biological rep3

city: Cleveland

first: Eain

middle: Anthony

last: Murphy

state: OH

department: Molecular Genetics

institute: Cleveland Clinic Foundation

description: HCMV infected Kasumi-3 cells were FACs sorted to remove eGFP positive cells, remaining cells were labeled with 4 thio uradine for 6 hrs for transcriptome analysis.

hyb_protocol: Following fragmentation, synthezided cRNA was hybridized ON on Affymetrix human gene array ST 2.0. arrays were washed and stained a the Affymetrix Fluidics Station 450.

scan_protocol: The chips were then  scanned using an Affymetrix Genechip Scanner 3000.

data_processing: The raw data was analized with Affymetrix GeneChip Command Console (AGCC) Software.

source_name: HCMV infected Kasumi-3 cells (96hpi) Sample 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA .

growth_protocol: Mock or HCMV infected Kasumi-3 cells were maitained in latency media for 96hrs.  eGFP negative cells were isolated.

extract_protocol: Total RNA was isolated using TRIAZOL reagent.  Thio containing RNA was used in a Biotin switch reaction. Biotinylated RNA was enriched over strepavidin beads and used for array labeling.

treatment_protocol: cells were labeled with either 4SU (mock) or 4TU (infected) for either 2 or 6 hrs respectively.

tag: cell line

value: TB40e GATA::UPRT IE2-t2a-eGFP Iinfected (96hpi)


title: UC6_d17_TGFb


title: HCMV infected Kasumi-3 cells, biological rep1

source_name: HCMV infected Kasumi-3 cells (96hpi) Sample 1


title: UC7_d17_non

value: unstimulated


title: UC2_d17_MC


title: UC12_d17_non


title: Mock infected Kasumi-3 cells, biological rep3

description: Mock infected Kasumi-3 samples were labeled with 4 thio uradine for 2 hrs and used as a negative control.

source_name: Mock infected Kasumi-3 cells Sample 3

value: Mock


title: Mock infected Kasumi-3 cells, biological rep2

source_name: Mock infected Kasumi-3 cells Sample 2


title: HCMV infected Kasumi-3 cells, biological rep2

source_name: HCMV infected Kasumi-3 cells (96hpi) Sample 2


title: UC2_d17_IFNy

value: interferon-gamma stimulated


title: UC6_d17_IFNy


title: 10hp

status: Public on Apr 23 2018

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

description: microRNA

data_processing:
demultiplexing: bcl2fastq
quality control: FastQC
trimming off the 3' adapter sequences: UEA sRNA WorkbenchV3.2
filtering: UEA sRNA WorkbenchV3.2; parameters: 17-25 nt in length, minimum abundance of at least 6 supporting reads, tRNA and rRNA sequences excluded.
mapping: the filtered reads were mapped to Sscrofa10.2 genome and miRBase 21.0, using miRCat tool embeded in UEA sRNA WorkbenchV3.2. The following parameters were applied - default animal parameters, except for: minimum abundance (6), minimum length (17 nt) and maximum length (25 nt).
differential expression analysis: DESeq2 (a Bioconductor R-project package)
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: FASTA files after filtering and adaptor trimming, generated with the use of UEA sRNA Workbench V3.2, for each sample. They include the number of reads of detected sequences.

organism: Sus scrofa

source_name: Hampshire high weight loin muscel tissue

extract_protocol:
The quality and quantity of the obtained RNA were checked on a NanoDrop 2000 spectrophotometer (Thermo Scientific; Wilmington, USA) and on a TapeStation 2200 instrument (RNAScreen Tape, Agilent, Perlan Technologies, Poland). Samples with RIN above 7.5 were used to construct libraries.
microRNA libraries were prepared with the use of NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs; E7300L), according the standard protocol. Briefly, the first step was the 3’ adaptor ligation, followed by hybridization with the Reverse Transcription Primer and ligation with the 5’ adaptor. The RNA-adaptor ligation products were subjected to reverse transcription. Then, PCR amplification with 12 different indexed primers was performed to allow further multiplexing of the samples. The amplified samples were purified and size-selected on a Novex 6% TBE PAGE gel (Invitrogen). After the overnight elution from the gel, the libraries were precipitated and purified with ethanol (POCH). Next, they were subjected to a concentration measurement with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and a size assessment with a 2200 TapeStation instrument (Agilent). The libraries were stored at -20°C at 10nM concentration until further use.

treatment_protocol: Immediately after slaughter, tissue samples were collected into RNAlater solution (Ambion, Thermo Fisher Scientific) and stored at -20°C

tag: breed

value: Hampshire

value: longissimus lumborum

tag: group

value: c

tag: loin weight

value: high weight loin

tag: platform

value: HiScanSQ (Illumina)

tag: gender

value: female

tag: age

value: 6 months


title: Mock infected Kasumi-3 cells, biological rep1

source_name: Mock infected Kasumi-3 cells Sample 1

tag: treatment


title: UC6_d3_MC

value: day 3


title: UC12_d17_IFNy

value: umbilical cord


title: UC7_d17_IFNy

value: day 17


title: UC7_d17_TGFb


title: Buruli_ulcer_ind7

city: New York

first: Yelena

last: Nemirovskaya

address: 1230 York Avenue

institute: Rockefeller University

hyb_protocol: As per manufacturer

scan_protocol: Generated following protocol of the genomic core facility of the Rockefeller University

data_processing:
CEL files were processed by Affymetrix Genotyping Console 3.0.1. Calls were generated using birdseed v2 algorithm.
Genotype Call: 0: homozygous for reference allele, 1: heterozygous, 2: homozygous for alternative allele; -1: no call

label: Biotin

source_name: blood cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from whole blood according to the Nucleon BACC2 Genomic DNA extraction protocol (GE Healthcare)

tag: tissue

value: whole blood

value: Female

tag: individual

value: Child (affected)

tag: disease state

value: Buruli Ulcer


title: UC7_d3_MC

value: Multi-factor combination stimulated


title: UC6_d17_non

value: unstimulated


title: UC2_d17_non


title: Buruli_ulcer_ind6

value: Male

value: Father

value: normal


title: Buruli_ulcer_ind3

value: Child


title: UC2_d3_MC


title: 9hp

description: microRNA

value: Hampshire

value: longissimus lumborum

value: c

value: high weight loin


title: UC12_d3_MC

value: day 3


title: 5pp

description: microRNA

source_name: Pietrain low weight loin muscel tissue

value: Pietrain

value: b

value: low weight loin

value: HiScanSQ (Illumina)

value: female

value: 6 months


title: 3pp

description: microRNA


title: UC6_d3_TGFb

value: umbilical cord

value: TGF-beta stimulated


title: UC12_d3_TGFb


title: 3hp

description: microRNA

source_name: Hampshire low weight loin muscel tissue

value: d


title: 8pp

description: microRNA


title: UC7_d3_TGFb


title: CSC - rep2

city: Berlin

first: Giovanni

last: Valenti

address: Robert-Roessle-Strasse 10

department: Cancer

institute: Max Delbrueck Center for Molecular Medicine

description: Gene expression profile of CSCs sorted from mammary gland tumors

hyb_protocol: Following fragmentation, 10 ug of aRNA samples were hybridized for 16 hr at 45°C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 7G

data_processing: The microarrays were RMA normalized in R statistics (http://www.R-project.org) using the Bioconductor libraries (http://www.bioconductor.org) with the software BRB-ArrayTools (http://linus.nci.nih.gov/BRB-ArrayTools.html)

source_name: Mammary gland tumors

label_protocol: Biotinylated aRNA samples were prepared according to the standard Affymetrix protocol from 100 ng of total RNA

growth_protocol: Single cell suspensions were obtained from mouse mammary gland primary tumors or control mammary glands and used for cell sorting

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA samples were further purified with Rnaesy Minikit. Quality and purity of RNA samples were assessed by Nanodrop and Bioanalyzer (Agilent) measurements before further processing

treatment_protocol: Samples were immediately processed for RNA extraction after sorting

tag: strain

value: FVB/N

value: mammary gland

tag: genotype

value: WAPCre-DNbcatn;HGF

tag: sorted cells

value: CSCs


title: Buruli_ulcer_ind4

value: whole blood

value: Female

value: Child

value: normal


title: 2hp

description: microRNA

value: Hampshire

value: longissimus lumborum


title: Buruli_ulcer_ind5

value: Mother


title: UC2_d3_TGFb

tag: tissue of origin

value: day 3


title: 8hp

description: microRNA

value: c

value: high weight loin

value: HiScanSQ (Illumina)

value: female


title: Buruli_ulcer_ind1

value: Child (affected)

value: Buruli Ulcer


title: 6pp

description: microRNA

source_name: Pietrain high weight loin muscel tissue

value: Pietrain

value: a

value: 6 months


title: Buruli_ulcer_ind2

value: whole blood


title: 1pp

description: microRNA


title: MEFs_GR-C3 knockin_Dex6hr_rep2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: GR-C3 knockin MEFs_100nM dex-treated_6 hours

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Total RNA was harvested for microarray analysis using the RNeasy Mini Kit (Qiagen) and RNase-Free DNase Kit (Qiagen) according to manufacturer's instructions from 3 biological replicates of vehicle-treated WT MEFs, Dex-treated WT MEFs, vehicle-treated GR-C3 knockin MEFs, and Dex-treated GR-C3 knockin MEFs.

tag: strain background

tag: genotype/variation

value: GR-C3 knockin

tag: cell type

value: embryonic fibroblasts

tag: treated with

value: 100nM Dex for 6 hrs


title: 1hp

description: microRNA

tag: breed

value: Hampshire

tag: group

value: d

value: low weight loin


title: UC12_d3_non

value: umbilical cord

tag: donor

tag: time point

value: day 3

value: unstimulated


title: MEFs_GR-C3 knockin_Dex6hr_rep3


title: CSC - rep1

value: FVB/N

value: mammary gland

value: WAPCre-DNbcatn;HGF

value: CSCs


title: 7pp

description: microRNA

value: Pietrain

value: longissimus lumborum

tag: loin weight

value: high weight loin

tag: platform

value: HiScanSQ (Illumina)

tag: gender

value: female

tag: age


title: 2pp

description: microRNA

tag: tissue

value: a

value: 6 months


title: MEFs_GR-C3 knockin_Con6hr_rep2

source_name: GR-C3 knockin MEFs_vehicle-treated_6 hours

value: GR-C3 knockin

value: embryonic fibroblasts

value: vehicle for 6hrs


title: MEFs_GR-C3 knockin_Dex6hr_rep1

value: 100nM Dex for 6 hrs


title: CAF - rep3

description: Gene expression profile of CAFs sorted from mammary gland tumors

tag: strain

value: CAFs


title: MEFs_GR-C3 knockin_Con6hr_rep1


title: CAF - rep1

tag: genotype


title: MEFs_GR-C3 knockin_Con6hr_rep3


title: TEC - rep2

description: Gene expression profile of TECs sorted from mammary gland tumors

tag: sorted cells

value: TEFs


title: UC2_d3_IFNy

tag: tissue of origin

value: umbilical cord

value: day 3

tag: treatment

value: interferon-gamma stimulated


title: MEFs_WT_Dex6hr_rep3

source_name: WT MEFs_100nM dex-treated_6 hours

tag: strain background

tag: genotype/variation

value: wild type


title: UC6_d3_IFNy

source_name: ucMSC


title: TEC - rep1

value: FVB/N

value: mammary gland

value: WAPCre-DNbcatn;HGF


title: MEFs_WT_Dex6hr_rep1

tag: cell type

tag: treated with


title: MEFs_WT_Con6hr_rep2

source_name: WT MEFs_vehicle-treated_6 hours


title: COF - rep2

description: Gene expression profile of COFs sorted from control mammary glands

source_name: Control mammary glands

value: WT

value: COFs


title: COF - rep3


title: Wt_3_VICs

city: Vari

first: George

last: Kollias

address: 34 Fleming Street

department: Institute of Immunology/Department of Physiology, School of Medicine

country: Greece

institute: BSRC "Alexander Fleming"/National and Kapodistrian University of Athens

description:
processed data file: metaseqr_colvip75ffdare_wt_vics.txt
processed data file: metaseqr_dare_wt_vics.txt

data_processing:
Initial analysis was performed within Ion Torrent server were the strand specific sequencing reads mapped (>90%) to their corresponding strand on the genome (BSRC Al. Fleming Genomics Facility).
The raw bam files were summarized to read counts table using the Bioconductor package GenomicRanges
The gene counts table was normalized for inherent systematic or experimental biases using the Bioconductor package DESeq after removing genes that had zero counts over all the RNA-Seq samples.
The resulting gene counts table was subjected to differential expression analysis using the Bioconductor package DESeq
All the above were performed through the Bioconductor package metaseqr
Genome_build: mm10
Supplementary_files_format_and_content: txt (tab seperated) files containing all the results from metaseqr analysis inlcuding expression per replicate, fold change compared to control and pvalues.

source_name: Valve Interstitial Cells

growth_protocol: SF cultures were performed as previously described (Aidinis V, et al. (2003) Functional analysis of an arthritogenic synovial fibroblast.Arthritis Res Ther 5(3):R140-57.). VICs cultures were established by enzymatic treatment of isolated aortic valve leaflets from 8-wk- old mice, as previously reported (Furtado MB, et al. (2014) Microarray profiling to analyse adult cardiac fibroblast identity. Genom Data 2:345–350.).

extract_protocol:
Ankle joints and aortic heart valves were collected, isolated and cultured for 4 passages from the following genotypes: wt, Tnf ARE/+ and Tnf ARE/+ ;Tnfrsf1b MCKO . 3 mice per genotype were used.
All samples were diluted to a mean concentration of approximately 100-150ng/μl and their quality was measured in the bioanalyzer (Agilent Technologies) using the Agilent RNA 6000 Nano Kit reagents and protocol(Agilent Technologies). RNA samples with RNA Integrity Number (RIN) were selected and further processed for library preparation and sequencing. Libraries were prepared with the 3’ mRNA-Seq Library Prep Kit Protocol for Ion Torrent (QuantSeq-LEXOGEN ™ Vienna, Austria) according to manufacturer’s instructions. Each library’s quality and quantity, was assessed in bioanalyzer using the DNA High Sensitivity Kit reagents and protocol (Agilent Technologies). The quantified libraries were pooled together in 12plex at a final concentration of 50pM. The pools were then processed, templated and enriched on an Ion Proton Chef instrument. Templating was performed, using the Ion PI™ IC200™ Chef Kit (ThermoFisher Scientific) and sequencing, with the Ion PI™ Sequencing 200 V3 Kit on Ion Proton PI™ V2 chips (ThermoFisher Scientific) according to commercially available protocols. 3’RNA-sequencing was performed on an Ion Proton™ System (Rothberg et al, 2011), according to the manufacturer's instructions.

value: Wild type

value: Valve Interstitial Cells


title: UC7_d3_IFNy


title: MEFs_WT_Con6hr_rep3


title: COF - rep1


title: Wt_3_SFs

description:
processed data file: metaseqr_colvip75ffdare_wt_sfs.txt
processed data file: metaseqr_dare_wt_sfs.txt

source_name: Synovial Fibroblasts

value: Synovial Fibroblasts


title: MEFs_WT_Dex6hr_rep2

value: embryonic fibroblasts


title: UC12_d3_IFNy


title: UC2_d3_non

value: unstimulated


title: Mix_sugar_time_4 replicate 1

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

institute: Centre of fungal biodiversity

hyb_protocol: Following fragmentation, 10 µg of cRNA was hybridized to Affymetrix A. niger Genome Gene chips (GPL6758). GeneChips were washed and stained in an automated process.

scan_protocol: GeneChips were scanned.

data_processing: Microarray data was analyzed using Affymetrix Expression Console software v1.4.1.46 with the normalized values in linear scale. The probe intensities were normalized for background by the robust multiarray average (RMA) method which makes use of only the perfect match probes. Gene expression values were calculated with the medianpolish summary method from the PM probes.

organism: Aspergillus niger

source_name: A. niger wild type grown on mix sugars 33 hours

label_protocol: Biotin-labeled antisense cRNA was produced from 2 µg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com).

growth_protocol: A. niger N402 wild type was pre-cultured in 1 L Erlenmeyer flasks in 200 mL complete medium (CM), pH 6.0, that contained Aspergillus minimal medium (MM) (de Vries R, et al., 2004. Appl Env Mic). The pre-cultures were inoculated with 106 spores/mL and incubated at 250 rpm for 16 h at 30°C

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen) and purified using TRIzol® Plus RNA Purification Kit (Sigma-Aldrich) according to the instructions of the manufacturer.

treatment_protocol: Mixture of 10 mM monomeric sugars (D-glucose, D-fructose, D-mannose, D-galactose, L-rhamnose, D-xylose, L-arabinose, D-galacturonic acid) and maltose (Sigma-Aldrich) was added into 50 mL MM in 250 mL Erlenmeyer flasks. The cultures were inoculated with mycelial aliquots from the pre-cultures (1 g wet-weight per flask) and incubated at 250 rpm, at 30°C. Samples from 12, 18, 24 and 33 h were used for microarrays.

value: Wild type N402


title: Mix_sugar_time_4 replicate 2


title: Wt_2_VICs


title: Mix_sugar_time_3 replicate 2

source_name: A. niger wild type grown on mix sugars 24 hours


title: Mix_sugar_time_2 replicate 1

source_name: A. niger wild type grown on mix sugars 18 hours


title: Mix_sugar_time_1 replicate 2

source_name: A. niger wild type grown on mix sugars 12 hours


title: Mix_sugar_time_1 replicate 1


title: LFD RWAT 2

city: Oxford

first: Haifei

last: Shi

state: Ohio

address: 700 E High St

department: Biology

institute: Miami University

description: total RNA

data_processing:
Remove Truseq3-SE adapter sequence using Trimmomatic (version 0.36)
Single-end sequencing reads were aligned to the mouse genome (ENSEMBL 84 release, GRCm38.p4) using RSEM (version 1.3.0)
Differential gene expression analysis was performed by DESeq2 (version 1.10.1) using the estimated gene-level counts from RSEM
Genome_build: RNA-Seq clean reads  were mapped to mouse genome (ENSEMBL 84 release, GRCm38.p4)
Supplementary_files_format_and_content: RSEM results (counts, TPMs, FPKMs)

source_name: LFD RWAT

extract_protocol:
RNA extraction using E.Z.N.A® Total RNA kit II (Omega Bio-tek)
Libraries were sequenced as single-end 75 bp on Illumina NextSeq500 sequencing system at Cofactor Genomics Inc (St. Louis, MO). Approximately 30 millions of reads were retrieved from each sample
Ribosomal RNA was removed by using TruSeq Standard Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina)

treatment_protocol: Male C57BL/6J mice at age of 6 weeks - 10 weeks fed either a low-fat diet or a high-fat diet.

value: retroperitoneal white adipose tissue

tag: Sex

value: male

tag: diet

value: standard rodent diet


title: LFD RWAT 3

description: total RNA


title: LFD RWAT 1

description: total RNA


title: CAF - rep2

value: CAFs


title: Mix_sugar_time_2 replicate 2


title: LFD IWAT 3

description: total RNA

source_name: LFD IWAT

value: inguinal white adipose tissue


title: HFD RWAT 1

description: total RNA

source_name: HFD RWAT

value: wild type

value: 45% high-fat diet


title: HFD RWAT 2

description: total RNA


title: HFD RWAT 3

description: total RNA


title: MEFs_WT_Con6hr_rep1

value: vehicle for 6hrs


title: Wt_2_SFs


title: UC6_d3_non

value: umbilical cord

tag: donor

tag: time point

value: day 3


title: HFD IWAT 3

description: total RNA

source_name: HFD IWAT


title: LFD IWAT 1

description: total RNA


title: Wt_1_VICs


title: HFD IWAT 2

description: total RNA


title: Wt_1_SFs


title: LFD EWAT 3

description: total RNA

source_name: LFD EWAT

value: epididymal white adipose tissue


title: HFD IWAT 1

description: total RNA


title: TNF_DeltaARE_ColVI_p75_f_vs_f_3_VICs

description: processed data file: metaseqr_colvip75ffdare_wt_vics.txt


title: LFD EWAT 1

description: total RNA


title: LFD IWAT 2

description: total RNA


title: TNF_DeltaARE_ColVI_p75_f_vs_f_3_SFs

description: processed data file: metaseqr_colvip75ffdare_wt_sfs.txt


title: HFD EWAT 2

description: total RNA

source_name: HFD EWAT


title: HFD EWAT 3

description: total RNA


title: HFD EWAT 1

description: total RNA


title: TNF_DeltaARE_ColVI_p75_f_vs_f_2_VICs


title: TNF_DeltaARE_ColVI_p75_f_vs_f_2_SFs


title: TNF_DeltaARE_3_VICs

description: processed data file: metaseqr_dare_wt_vics.txt

value: TNF-DeltaARE


title: TNF_DeltaARE_ColVI_p75_f_vs_f_1_VICs

value: Valve Interstitial Cells


title: TNF_DeltaARE_ColVI_p75_f_vs_f_1_SFs

value: Synovial Fibroblasts


title: LFD EWAT 2

description: total RNA


title: TNF_DeltaARE_2_SFs

description: processed data file: metaseqr_dare_wt_sfs.txt


title: TNF_DeltaARE_3_SFs


title: TNF_DeltaARE_2_VICs


title: TNF_DeltaARE_1_VICs


title: 10 µM CC-671 (24hr) - 1

city: La Jolla

first: Samuel

last: Danziger

state: CA

address: 10300 Campus Point Dr

institute: Celgene

data_processing:
HTSeq package was used to quantify gene expression level for each gene locus and annotation file used was "gencode.v18" (http://www.gencodegenes.org/).
Differential gene expression analysis as a result of treatment was carried out using R package “edgeR”,  genes with multiple test adjustment (“BH”) p.value < 0.05, absolute fold change >=2 are considered significant. A coverage filter (>=1 sample has >=50 read counts) was used to remove low coverage genes.
To identify pathways impacted by compound treatment, Gene Set Enrichment Analysis was carried out MSigDB canonical pathway collection C2.CP genesets (www.broadinstitute.org/gsea/msigdb ) was used, adjust.p.value < 0.05 was considered significant.
Global splicing effect of the compound treatment was assessed by two measures. First, exon rate (bases mapped to coding region divided by bases aligned) was calculated for each sample, comparison of exon rate between treated and control was carried out by Kruskal.test. Second, PSI (percent of spliced in, Fig S4) of “exon skipping/inclusion” events was calculated. This was done via MISO software (http://genes.mit.edu/burgelab/miso/). PSI values from treated and control samples were compared.
To identify differentially splicing affected by compound treatment, "DEXSeq" R package was used. Expression of exon bin  was quantified using HTSeq, annotation database used was "gencode.v18" ,  differential exon usage identification was carried out using DEXSeq. Exons with adj.p (“BH”) < 0.05, and absolute fold change >=2 are considered significant. Significant hits were visualized using DEXSeq plotting utilities and genome browser. To prioritize hits of DEXSeq results, following criteria were used to : log2(fold change)>=1,  adj.p value < 0.0001,  exon bin size >= 100,  raw read counts >= 50  for at least one sample and gene expression is not significantly changed by compound treatment.
To identify pathways over-represented by genes whose splicing are changed by treatment, R package “GSEABase” (hypergeometric test) was used, adj.p.value (“BH”)  < 0.05, gene sets used was MSigDB canonical pathway collection C2.CP collection.
‘Spliced Transcripts Alignment to a Reference (STAR)’ was used to align reads to human genome hg19 with default settings
All analyses were carried out using statistics software R (www.r-projects.org) unless stated otherwise.
Genome_build: GRCh37.73
Supplementary_files_format_and_content: Illumina

growth_protocol: Triple negative breast cancer (TNBC) line CAL51 was grown in DMEM medium containing 10% fetal bovine serum

extract_protocol:
RNeasy kit, Poly-A selection.
Strand-specific RNA library construction were performed, followed by multiplexing indexed libraries and sequencing on the HiSeq 2500 with 2x100 bp read lengths

treatment_protocol: The growing cells were treated by CC-671 in three biological replicates at the following concentrations and time intervals.  The treatment time points were 6 hour and 24 hour. Concentration of compounds used was 3 and 10 uM.

value: Breast cancer cell line

tag: passages

tag: cell line

tag: cytogenetics

value: Near-diploid karyotype with 28% tetraploidy


title: 10 µM CC-671 (6hr) - 1

source_name: Triple negative breast cancer (TNBC) line CAL51


title: 10 µM CC-671 (6hr) - 2


title: 10 µM CC-671 (6hr) - 3


title: 10 µM CC-671 (24hr) - 2


title: UC7_d3_non

value: unstimulated


title: 3 µM CC-671 (24hr) - 2


title: 3 µM CC-671 (6hr) - 3


title: 10 µM CC-671 (24hr) - 3


title: 3 µM CC-671 (6hr) - 2


title: 3 µM CC-671 (6hr) - 1


title: DMSO (24hr) - 2

value: DMSO (24hr)


title: MLM-22

city: Parkville

first: Andrew

last: Lonsdale

state: VIC

address: 50 Flemington Rd

country: Australia

institute: Murdoch Children's Research Institute

description: B-cell Acute Lymphoblastic Leukaemia (B-ALL) samples with a P2RY8-CRLF2 fusion gene

data_processing:
Fastq files were generated using the bcl to fastQ converter 2.17.
Fusion genes called with JAFFA v1.09
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated text file of fusion calls from all samples (column 9 "spanning reads" is a measurement of abundance, given as the number of reads spanning the fusion breakpoint)

source_name: bone marrow

extract_protocol:
RNA were extracted using QIAGEN RNeasy micro kit.
TruSeq stranded total RNA with RiboZero rRNA depletion

tag: fusion

tag: sample source

value: diagnostic

value: B-cell ALL


title: EKL-7-8


title: EKL3-26


title: DMSO (24hr) - 1


title: 3 µM CC-671 (24hr) - 3


title: EKL15-5


title: DMSO (6hr) - 2

value: DMSO (6hr)


title: DMSO (6hr) - 1


title: EKL-6-8


title: 3 µM CC-671 (24hr) - 1


title: TNF_DeltaARE_1_SFs

tag: genotype

tag: strain

tag: tissue


title: m3_Pb_GSK

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Tophat2 and the UCSC mm9 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique RefSeq gene using the GenomicRanges package in R/Bioconductor and normalized to reads per kilobase per million (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: Annotation file containing RPKM normalized read counts for each gene for each sample.

molecule: polyA RNA

source_name: ex vivo cultured B cells

extract_protocol:
For each cell type total RNA was extracted using the Qiagen RNeasy Kit
500 ng of total RNA was used as input for the KAPA Biosystems Stranded mRNA-seq kit with polyA selection beads.

treatment_protocol: CD43- B cells were isolated from wild-type mice by CD43 depletion on a MACS column and cultured ex vivo in the presence of LPS, Il2, and Il5 with either DMSO or GSK343.

value: female

tag: sorting markers

tag: stimulation

value: LPS, Il2, Il6

tag: drug treatment

value: Plasmablasts


title: m3_Pb_DMSO

value: LPS, Il2, Il5

value: DMSO

tag: cell type


title: m3_naive

value: B cells


title: m3_actb_GSK

value: Activated B cells


title: m3_actB_DMSO


title: m2_Pb_GSK


title: m2_Pb_DMSO


title: m2_actb_GSK


title: m2_actB_DMSO


title: tgs1/rnt1 RNA-seq

first: Nicholas

last: Proudfoot

address: South Parks Road

country: United Kingdom

institute: Sir William Dunn School of Pathology,  University of Oxford

data_processing:
For RNA-seq sequencing, single-end reads were mapped to sacCer3 genome using two-step alignments. First, the reads were aligned with TopHat. Second, the resulting unmapped reads from the first step were then extracted and aligned with Bowtie2,with --very-sensitive-local and --local options.
genome build: sacCer3
processed data files format and content: BigWig file containing read densities from RNA-seq experiments.

organism: Saccharomyces cerevisiae

source_name: RNT1/TGS1 deletion strain

growth_protocol: all strains were grown in YPD medium at 25C with exception of Cbp20-myc and Rnt1-myc which grew at 30C

extract_protocol:
RNA was iolated using standard hot phenol method
RNA-seq libraries were prepared using Ion Total RNA-seq Kit v2 (Thermofisher)

value: MATa, ura3-1, ade2-1, his3-11,5,trp1delta, RNT1::TRP, TGS1::HIS

tag: analysis

value: RNA-seq, total RNA


title: tgs1 RNA-seq

source_name: TGS1 deletion strain

value: MATa, ura3-1, ade2-1, his3-11,5,trp1delta, TGS1::HIS


title: WT_for_rnt1 RNA-seq

source_name: BMA 64

value: MATa, ura3-1, ade2-1, his3-11,5,trp1delta


title: Mix_sugar_time_3 replicate 1

value: Wild type N402


title: rnt1/cbp80 RNA-seq

source_name: RNT1/CBP80 deletion strain

value: MATa, ura3-1, ade2-1, his3-11,5,trp1delta, RNT1::TRP, CBP80::HIS


title: m2_naive

tag: Sex


title: Female Cynoglossus semilaevis liver in high salinity 3

city: QINGDAO

first: YUFENG

last: SI

state: SHANDONG

address: 5 YUSHAN ROAD

department: COLLEGE OF FISHERIES

institute: OCEAN UNIVERSITY OF CHINA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to the reference genome using TopHat v2.0
RPKM, Reads Per Kilobase of exon model per Million mapped reads,were calculated using a protocol from Mortazavi et al., Nature methods, 2008.
Differential expression analysis of two groups (three biological replicates per group) was performed using the DESeq,padj<0.05, Log2Foldchange>1
Genome_build: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6.
Supplementary_files_format_and_content: excel files include FPKM values for each sample

organism: Cynoglossus semilaevis

source_name: liver

growth_protocol: Fish were reared in commercial fish ponds (5m*5m*1m) for 10 months, under the controlled conditions (20 ± 0.5 ℃; 14:10 h light/dark cycle; O2≥4 ng/ml; 30 ppt), and fed on a prepared diet.

extract_protocol:
Livers from three female individuals in each tank was dissected, immediately frozen in liquid nitrogen, and stored at -80 °C until RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: low salinity 15 ppt, high salinity 30 ppt for 60 days

tag: age

value: 10 months

value: liver


title: m1_Pb_GSK


title: cbp20/80 RNA-seq

source_name: CBP20/CBP80 deletion strain

value: MATa, ade2, ade3, his3, leu2-3, 112 rp1 ura3 CBP80::TRP1 CBP20::HIS


title: Wt for cbp20/80D RNA-seq

source_name: WT for CBP20/CBP80 deletion strain

value: MATa, ade2, ade3, his3, leu2-3, 112 rp1 ura3


title: EKL13-7

value: diagnostic

value: B-cell ALL


title: Female Cynoglossus semilaevis liver in high salinity 2

value: female


title: Female Cynoglossus semilaevis liver in high salinity 1


title: m1_Pb_DMSO

value: LPS, Il2, Il5

value: Plasmablasts


title: Female Cynoglossus semilaevis liver in low salinity 3


title: Cbp20-myc ChIP Rep2

description: MATa his3Δ1, leu2Δ0, met15Δ0,  ura3Δ0CBP80-myc13::NAT

library_source: genomic

data_processing:
For RNA-seq sequencing, single-end reads were mapped to sacCer3 genome using two-step alignments. First, the reads were aligned with TopHat. Second, the resulting unmapped reads from the first step were then extracted and aligned with Bowtie2,with --very-sensitive-local and --local options.
For Chip-seq, paired-end reads were mapped to the sacCer3 genome using the Bowtie2 . Uniquely mapped reads with a mapping quality ≥ 30 were retained for further analysis. Peaks were called using MACS2 with default options. Peaks with q-value below 0.05 were retained .
Genome_build: sacCer3 (April 2011)
Supplementary_files_format_and_content: BigWig file containing read densities from RNA-seq experiments.

source_name: Cbp20-myc tagged strain

extract_protocol:
RNA was iolated using standard hot phenol method; ChIP samples were preapred usig standard ChIP protocol
RNA-seq libraries were prepared using Ion Total RNA-seq Kit v2 (Thermofisher) while ChIP libraries were prepared using NEBNext ChIP-seq Library Prep

tag: genotype/variation

value: MATa his3{delta}1, leu2{delta}0, met15{delta}0,ura3{delta}0CBP80-myc13::NAT

tag: chip antibody

value: anit-myc (abcam, ab9132)


title: Rnt1-myc ChIP rep2

description: MATa his3Δ1, leu2Δ0, met15Δ0,  ura3Δ0RNT1-myc13::NAT

source_name: Rnt1-myc tagged strain

value: MATa his3{delta}1, leu2{delta}0, met15{delta}0,ura3{delta}0RNT1-myc13::NAT


title: m1_actB_DMSO

value: DMSO

value: Activated B cells


title: Female Cynoglossus semilaevis liver in low salinity 1


title: Cbp20-myc ChIP

data_processing:
For Chip-seq, paired-end reads were mapped to the sacCer3 genome using the Bowtie2 . Uniquely mapped reads with a mapping quality ≥ 30 were retained for further analysis. Peaks were called using MACS2 with default options. Peaks with q-value below 0.05 were retained .
genome build: sacCer3
processed data files format and content: bed file with called peaks

extract_protocol:
ChIP samples were prepared using standard ChIP protocol
ChIP libraries were prepared using NEBNext ChIP-seq Library Prep (NEB)

value: MATa his3delta_1, leu2delta_0, met15delta_0,  ura3delta_0CBP80-myc13::NAT

value: ChIP with anti-myc antibody

tag: antibody

value: anti-myc antibody (abcam ab9132)


title: m1_naive

value: B cells


title: Female Cynoglossus semilaevis liver in low salinity 2

value: 10 months

value: liver


title: Rnt1-myc ChIP

value: MATa his3delta_1, leu2delta_0, met15delta_0,  ura3delta_0RNT1-myc13::NAT


title: rnt1 RNA-seq

source_name: RNT1 deletion strain

value: MATa, ura3-1, ade2-1, his3-11,5,trp1delta, RNT1::TRP

value: RNA-seq, total RNA


title: m1_actb_GSK

value: female


title: DPC_estradiol_rep1

status: Public on Apr 22 2018

city: Edogawa-ku

first: Yujiro

last: Endo

state: Tokyo

address: 7-2-1 Hirai

department: Research & Development Headquarters

country: Japan

institute: Lion Corporation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip Human Genome U133 Plus 2.0 Array. Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis were calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: DPC, treated estradiol

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3' IVT Express Kit（Affymetrix) from 250 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: DPCs were cultured in Dulbecco's modified eagle medium without phenol red containing penicillin/streptomycin  at 37°C in 5% CO2.

extract_protocol: Extraction of total RNA was performed using RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: DPCs were treated with 0.1% dimethyl sulfoxide (as control) or 10nM beta-estradiol for 24 hour.

value: dermal papilla cell

tag: race

value: caucasian

tag: gender

value: Female

tag: treatment

value: 10nM beta-estradiol


title: DPC_control_rep3

source_name: DPC, control

value: 0.1% Dimethyl sulfoxide


title: DPC_control_rep2


title: DPC_estradiol_rep3


title: DPC_estradiol_rep2


title: Wildtype_RNAseq_Rep1

first: Frank

last: Tedeschi

address: 10900 Euclid AVE, cc/ Accounts Payable

institute: Case Western Reserve University

description:
RNAseq_FPKM_Dbp2null_Wt.txt
FPKM_Wt_1
Ribo depleted total RNA

data_processing:
Basecalling with Illumina Casava software
3' adapter trimming and collapsing with FastX-toolkit
FastQ quality Trimmer
Transcriptome alignment with TopHat
Analyzed by Cufflinks and EdgeR.
Genome_build: SacCer3
Supplementary_files_format_and_content: .txt (Gene name, FPKM)

source_name: Whole Cells Wildtype

growth_protocol: Cells were grown to an OD600 of ~ 0.4 in YPD medium

extract_protocol:
Cells were rapidly sedimented and snap-frozen on dry ice. Whole cell extracts were generated by breaking the cells with glass beads. Detailed information available in the Methods section of the article.
cDNA libraries were prepared using Illumina ScriptSeq Complete Gold Kit for yeast (BGY1306) and ScriptSeq Index PCR Primers set 1 (RSBC10948) according to the manufacturers protocol with the following adjustments, in order to avoid depletion of short RNAs including snoRNAs. Purification of the rRNA-depleted samples was performed by ethanol precipitation instead of AMPure bead purification. cDNA was purified by the MineElute PCR Purification kit (Qiagen) in place of the AgencourtAMPure XP system

tag: strain (genetic background)

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

value: Wildtype

tag: temperature

value: 30 dgC


title: iCLIP_Dbp2p_HTBH_Replicate2

description: Dbp2p-protected RNA

data_processing:
Basecalling with Illumina Casava software
3' adapter trimming and collapsing with FastX-toolkit
FastQ quality Trimmer
Transcriptome alignment with TopHat
Further read analyses by custom scripts in Rstudio. More detailed information on additonal software in the methods section of the accompanying article.
Genome_build: SacCer3
Supplementary_files_format_and_content: files in .txt format (columns 1-6: chr:1; position:2; strand:3; sequence:4; gene:5; normalized counts:6)

source_name: Whole Cells

growth_protocol: Cells were grown to an OD600 of ~ 1.0 in YPD medium

extract_protocol:
Cells were rapidly sedimented and snap-frozen on dry ice. Whole cell extracts were generated by breaking the cells with glass beads. Detailed information available in the Methods section of the article.
iCLIP

treatment_protocol: Cells were irradiated with UV light prior to harvesting

value: Strain BTY140. MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 DBP2-HTBH:kanMX6

tag: ip reagent

value: affinity pull down using a HIS-Biotin Tag


title: iCLIP_Dbp2p_HTBH_Replicate1

description: Dbp2p-protected RNA


title: dbp2null_RNAseq_Rep1

description:
RNAseq_FPKM_Dbp2null_Wt.txt
FPKM_D2n_1
Ribo depleted total RNA

source_name: Whole Cells dbp2Δ

value: Strain BTY115. dbp2{delta} MATa dbp2::KanMx ura3{delta}0 leu2{delta}0 his3{delta}0 TRP1 met- lys{delta}

tag: genotype


title: dbp2null_RNAseq_Rep2

description:
RNAseq_FPKM_Dbp2null_Wt.txt
FPKM_D2n_2
Ribo depleted total RNA


title: Wildtype_RNAseq_Rep2

description:
RNAseq_FPKM_Dbp2null_Wt.txt
FPKM_WT_2
Ribo depleted total RNA


title: DPC_control_rep1


title: adj. normal prostate sample, patient 15

first: Klaus

last: Jung

address: Schumannstr. 20/21

department: Dept. of Urology

institute: University Hospital Charité

hyb_protocol: cRNA were hybridized on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained according to the standard Affymetrix protocol

scan_protocol: After hybridization the GeneChips were scanned according to the standard Affymetrix protocol

data_processing: Affymetrix Expression Console Software with default analysis settings were used to generate corresponding MAS5 CHP files. The CHP-files were analyzed by Genespring (vers.12.6) software (normalization: shift to 75 percentile; baseline transformation: median of all samples)

source_name: prostate

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

extract_protocol: Isolation according to the instruction using RNeasyMini Kit (Qiagen, Hilden, Germany; Cat.no. 74104)

treatment_protocol: Immediate stabilization of tissue after surgery in RNAlater RNA Stabilization Reagent (Qiagen, Hilden, Germany; Cat.no. 76104)

tag: individual

value: patient 15

tag: disease state

value: prostate cancer

tag: tissue

value: male


title: primary PCa, patient 10

value: patient 10

value: PCa

tag: tumor staging

tag: grading


title: adj. normal prostate sample, patient 14

value: patient 14

tag: Sex


title: primary PCa, patient 13

value: patient 13

tag: age


title: primary PCa, patient 14


title: adj. normal prostate sample, patient 12

value: patient 12


title: primary PCa, patient 8

value: patient 8


title: adj. normal prostate sample, patient 10


title: primary PCa, patient 9

value: patient 9


title: primary PCa, patient 15


title: adj. normal prostate sample, patient 7

value: patient 7


title: primary PCa, patient 7


title: adj. normal prostate sample, patient 11

value: patient 11


title: adj. normal prostate sample, patient 8


title: adj. normal prostate sample, patient 9


title: primary PCa, patient 12


title: primary PCa, patient 11


title: adj. normal prostate sample, patient 13


title: adj. normal prostate sample, patient 4

value: patient 4


title: adj. normal prostate sample, patient 5

value: patient 5


title: adj. normal prostate sample, patient 3

value: patient 3


title: adj. normal prostate sample, patient 6

value: patient 6


title: adj. normal prostate sample, patient 2

value: patient 2


title: Transcriptional effects after the expression of MYB110 gene

city: Tsukuba

first: Akira

last: Takahashi

address: 2-1-2, Kannnondai

institute: National Institute of Agrobiological Sciences

hyb_protocol: Cy3-labelled cRNA and Cy5-labelled cRNA (825ng each) were mixed, fragmented and hybridized with the rice 4x44K microarray for 17 hours at 65°C using the Agilent Gene Expression Hybridization kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 4x44k array slides. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted.

organism: Oryza sativa

source_name: DEX-treated GVG-MYB110 calli

label_protocol: 400 ng of total RNAs were reverse-transcribed and labelled using Agilent's Quick Amp Labeling Kit following the manufacturer's instructions. Labelled cRNAs were purified with the Qiagen RNeasy Mini Kit.

growth_protocol: Transegenic calli of GVG-MYB30, GVG-MYB55, GVG-MYB110 and empty vector were cultured in N6D plates at 25°C.

extract_protocol: Total RNA was isolated from rice tissues by using Isogen (Nippongene) and digested with RNase-free DNase (Qiagen) to remove DNA contamination. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The calli were transferred to 2-ml plastic tubes with screw caps (0.5-ml fresh medium), and maintained in suspension for 18 h at 25°C with gentle shaking at 100 rpm. Dexamethasone (DEX) was used at 10 mM, starting from a 10 mM stock solution in ethanol. To avoid the effects of phenylpropanoid metabolic changes induced by MYB induction, we analyzed the transcript level at 4 h after DEX application.

tag: cultivar

value: japonica

tag: genotype/variation

value: expressing MYB110 gene

tag: cell type

value: calli

tag: treated with

value: 10 mM DEX for 4hrs

source_name: ethanol-treated GVG-MYB110 calli

value: ethanol for 4hrs


title: primary PCa, patient 6

value: prostate cancer

value: PCa

value: male


title: Transcriptional effects after the DEX-treatment

description: vector control

source_name: DEX-treated empty vector calli

value: vector control

source_name: ethanol-treated empty vector calli


title: primary PCa, patient 5


title: primary PCa, patient 4


title: adj. normal prostate sample, patient 1

value: patient 1


title: primary PCa, patient 3


title: DHA + DOX (60uM DHA+4.1x10-7 DOX) rep 4

status: Public on Apr 21 2018

city: Edmonton

first: Marnie

last: Newell

state: AB

address: 4-031 LKS Bldg, University of Alberta

department: Nutrition

country: Canada

institute: University of Alberta

description: Gene expression data from MDA-MB-231 Cells under DHA +DOX treatment experimental conditions

hyb_protocol: Microarrays were washed and stained in the Affymetrix Fluidics station 450 (fluidics protocol FS450_0002)

scan_protocol: GeneChips were scanned on the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Partek Genomics Suite

source_name: MDA-MB-231 cells, DHA+ DOX treated

label_protocol: 500ng samples were prepared according to the standard Ambion protocol for Ambion Wt kit

growth_protocol: Cells were seeded in 12 well plates at 1.5 x 10^5 cells/ mL and grown to 80% confluence

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

treatment_protocol: All cells were supplemented with control fatty acid background (40 uM OA and 40 uM LA) and subjected to 4 conditions: control OALA (72h), DHA (60uM, 72 h), DHA (60uM, 72 h) + DOX (final 24 h) or DOX (OALA, 72 H and DOX final 24h)

tag: gender

value: female

tag: strain

value: mammary gland /breast

value: breast cancer epithelial cells

tag: tumor

value: adenocarcinoma


title: DOX (40uM OA/ 40uM LA +4.1x10-7 DOX) rep 1

description: Gene expression data from MDA-MB-231 Cells under DOX treatment experimental conditions

source_name: MDA-MB-231 cells, DOX treated


title: DHA (60uM DHA) rep 3

description: Gene expression data from MDA-MB-231 Cells under DHA treatment experimental conditions

source_name: MDA-MB-231 cells, DHA treated


title: DOX (40uM OA/ 40uM LA +4.1x10-7 DOX) rep 2


title: primary PCa, patient 2


title: DHA + DOX (60uM DHA+4.1x10-7 DOX) rep 1


title: Control (40uM OA/40uM LA) rep 4

description: Gene expression data from MDA-MB-231 Cells under control experimental conditions

source_name: MDA-MB-231 cells, control conditions


title: primary PCa, patient 1


title: Control (40uM OA/40uM LA) rep 3


title: DHA + DOX (60uM DHA+4.1x10-7 DOX) rep 3


title: Transcriptional effects after the expression of MYB55 gene

source_name: DEX-treated GVG-MYB55 calli

value: expressing MYB55 gene

source_name: ethanol-treated GVG-MYB55 calli


title: DHA (60uM DHA) rep 4


title: DOX (40uM OA/ 40uM LA +4.1x10-7 DOX) rep 4


title: DHA + DOX (60uM DHA+4.1x10-7 DOX) rep 2


title: DHA (60uM DHA) rep 2


title: DMS-MaPSeq of purified cspA mRNA at 10°C with 0.1mM CspA protein, rep 2

city: San Francisco

first: Yan

last: Zhang

address: 600 16th Street

institute: UC San Francisco

description: DMS-modified mRNA purified from in vitro transcription reaction

data_processing:
Basecalls performed using Casava versions 1.6 or 1.7.
Sequenced reads were trimmed for adaptor sequence.
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded.
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1.
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read.
For DMS-MaPSeq, reads were aligned to the 5’UTR of cspA using bowtie2 and an alignment seed of 12nt.  Low sequence quality bases (Q score < 20%) and missing bases due to truncated reads were set to question marks. Reads that consisted of more than 20% question marks were filtered out. Only mutations that agreed between the forward and the reverse read were considered true mutations. Mutation rate per base was calculated as number of reads with a mutation at the base divided by total number of reads covering the base.
Genome_build: NC000913.2
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).
Supplementary_files_format_and_content: Txt files are processed data for DMS-MaPseq with two columns: first column containing chromosome positions (relative to transcription start site (1) of cspA) and second column containing the mutation rate.

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker.

extract_protocol:
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction.
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014).

treatment_protocol: For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion).

tag: treatment

value: 0.1mM CspA protein

tag: temperature


title: DMS-MaPSeq of purified cspA mRNA at 10°C with 0.1mM CspA protein, rep 3


title: DMS-MaPSeq of purified cspA mRNA at 10°C with 0.1mM CspA protein, rep 4


title: DOX (40uM OA/ 40uM LA +4.1x10-7 DOX) rep 3


title: DMS-MaPSeq of purified cspA mRNA at 10°C, rep 4


title: DMS-MaPSeq of purified cspA mRNA at 10°C, rep 3


title: DMS-MaPSeq of purified cspA mRNA at 10°C with 0.05mM CspA protein

value: 0.05mM CspA protein


title: Transcriptional effects after the expression of MYB30 gene

source_name: DEX-treated GVG-MYB30 calli

value: japonica

value: expressing MYB30 gene

source_name: ethanol-treated GVG-MYB30 calli


title: DMS-MaPSeq of purified cspA mRNA at 37°C, rep 2


title: DHA (60uM DHA) rep 1


title: Control (40uM OA/40uM LA) rep 1


title: Control (40uM OA/40uM LA) rep 2


title: Oligo-P22-H02

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

data_processing:
Paired-end, 38-base reads were mapped to the UCSC hg19 human transcriptome using Bowtie with parameters "-q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 -S -p 6". Expression values were calculated by   RSEM v1.2.3 in paired-end mode  using parameters "--estimate-rspd --paired end -sam -p 6", from which TPM values for each gene  were extracted.
For each cell, we quantified two quality measures: the number of genes for which at least one  read was mapped, and the average expression level of a curated list of housekeeping genes. We then conservatively excluded all cells with either fewer than 3,000 detected genes or an average housekeeping expression (E, as defined above) below 2.5.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing TPM values ( transcript-per-million reads) for 23,686 analyzed genes (rows), across 4058 glioma cells (columns, sample names indicated at the top row).

source_name: Glia single cell

growth_protocol: (for cell culture samples only): H3K27M cell cultures  were grown  as gliomaspheres  in Tumor Stem Medium (TSM) base supplemented with B27 Minus Vitamin  A, EGF, FGF, PDGFA, PDGFB and heparin  (29). All GBM cell cultures were grown as gliomaspheres (GS) in  Neurobasal  Medium,  supplemented  with  N2  supplement,  B27  supplement,  Glutamax, Pen/Strep  (all  Life  Technologies),  EGF  and  FGF  (Shenandoah Biotechnology  INC).  For   adherent conditions (DGC),  cells  were  either  (i)  cultured  in  TSM  base  supplemented  with  7.5%  or  10%  Fetal  Bovine Serum  (Atlas  Biologicals)  in  TC-treated  flasks  or  (ii) cultured  in  gliomasphere  TSM  base  supplemented with  B-27  Minus  Vitamin  A  +/-  EGF,  FGF,  PDGFA,  PDGFB  and  heparin  in  non-TC  treated  flasks.

extract_protocol:
RNA from single cells was first purified with Agencourt  RNAClean XP beads (Beckman Coulter)
Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli  2014) with the following modifications.oligo-dT were used to prime reverse transcription with  Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle  PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent  Agencourt AMPure XP bead purification as described. Libraries were tagmented using the  Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon  request). Libraries from 384 cells with unique barcodes were combined and sequenced using a  NextSeq 500 sequencer (Illumina).
single cell RNA-seq

treatment_protocol: (for human tumor samples only): Fresh tumor tissue was minced with a scalpel and enzymatically dissociated using a gentle papain-based brain tumor dissociation kit (Miltenyi Biotec). Large pieces of debris were removed with a 100 micron strainer, and dissociated cells were layered carefully onto a 5mL density gradient (Lympholyte-H, Cedar Lane labs), which was centrifuged at 2,000 rpm for 10 min at room temperature to pellet dead cells and red blood cells. The interface containing live cells was saved and used for staining and flow cytometry. Tumor cells were blocked in 1% bovine serum albumin in Hanks buffered saline solution (BSA /  HBSS), and then stained first with CD45-Vioblue direct antibody conjugate (Miltenyi Biotec) for  30 min at 4C. Cells were washed with cold PBS, and then resuspended in 1 mL of BSA / HBSS  containing 1uM calcein AM (Life Technologies) and 0.33uM TO-PRO-3 iodide (Life  Technologies) to co-stain for 30 min before sorting. Fluorescence-activated cell sorting was  performed on FACSAria Fusion Special Order System (Becton Dickinson) using 488nm (calcein  AM, 530/30 filter), 640nm (TO-PRO-3, 670/14 filter), and 405nm (Vioblue, 450/50 filter) lasers.   Fluorescence-minus-one controls were included with all tumors, as well as heat killed controls in  early pilot experiments, which were crucial to ensure proper identification of the TO-PRO-3  positive compartment and ensure sorting of the live cell population. Standard, strict forward  scatter height versus area criteria were used to discriminate doublets and gate only singlets.  Viable cells were identified by staining positive with calcein AM but negative for TO-PRO-3.  Single cells were sorted into 96-well plates containing cold buffer TCL buffer (Qiagen)  containing 1% beta-mercaptoethanol, snap frozen on dry ice, and then stored at -80C prior to  whole transcriptome amplification, library preparation and sequencing.

tag: sample type

value: cell culture


title: Oligo-P22-H05


title: Oligo-P22-H06


title: Oligo-P22-H08


title: Oligo-P22-G12


title: Oligo-P22-H03


title: Oligo-P22-H09


title: Oligo-P22-G11


title: Oligo-P22-G05


title: Oligo-P22-G07


title: Oligo-P22-G04


title: Oligo-P22-G01


title: Oligo-P22-G03


title: Oligo-P22-F10


title: Oligo-P22-F09


title: Oligo-P22-F12


title: Oligo-P22-F08


title: Oligo-P22-G02


title: Oligo-P22-F07


title: Oligo-P22-F05


title: Oligo-P22-F01


title: Oligo-P22-F03


title: Oligo-P22-E11


title: Oligo-P22-F04


title: Oligo-P22-E12


title: Oligo-P22-E09


title: Oligo-P22-E08


title: Oligo-P22-E05


title: Oligo-P22-E07


title: Oligo-P22-D01


title: Oligo-P22-D08


title: Oligo-P22-D06


title: Oligo-P22-C12


title: Oligo-P22-D10


title: Oligo-P22-D09


title: Oligo-P22-D07


title: Oligo-P22-C09


title: Oligo-P22-C10


title: Oligo-P22-C06


title: Oligo-P22-C03


title: Oligo-P22-C02


title: Oligo-P22-B12


title: Oligo-P22-E02


title: Oligo-P22-C01


title: Oligo-P22-B10


title: Oligo-P22-C11


title: Oligo-P22-E06


title: Oligo-P22-A11


title: Oligo-P22-A12


title: Oligo-P22-A10


title: Oligo-P22-B06


title: Oligo-P22-B02


title: Oligo-P22-A09


title: Oligo-P22-A04


title: Oligo-P22-A03


title: Oligo-P02-H09


title: Oligo-P02-H11


title: Oligo-P02-H10


title: Oligo-P22-C04


title: Oligo-P22-A01


title: Oligo-P02-H07


title: Oligo-P02-H02


title: Oligo-P22-C07


title: Oligo-P02-G11


title: Oligo-P02-H05


title: Oligo-P02-H04


title: Oligo-P02-G09


title: Oligo-P02-G07


title: Oligo-P02-G12


title: Oligo-P02-G10


title: Oligo-P02-G05


title: Oligo-P02-G06


title: Oligo-P22-B09


title: Oligo-P22-B08


title: Oligo-P22-B05


title: Oligo-P02-G04


title: Oligo-P02-G02


title: Oligo-P02-G03


title: Oligo-P02-G01


title: Oligo-P02-F07


title: Oligo-P02-F09


title: Oligo-P02-H08


title: Oligo-P02-F06


title: Oligo-P02-F02


title: Oligo-P02-E12


title: Oligo-P02-F10


title: Oligo-P02-E11


title: Oligo-P02-F04


title: Oligo-P02-E08


title: Oligo-P02-E09


title: Oligo-P02-E10


title: Oligo-P02-E05


title: Oligo-P02-E03


title: Oligo-P02-E06


title: Oligo-P02-E02


title: Oligo-P02-E04


title: Oligo-P02-D11


title: Oligo-P02-D08


title: Oligo-P02-D06


title: Oligo-P02-D07


title: Oligo-P02-D05


title: Oligo-P02-F12


title: Oligo-P02-D09


title: Oligo-P02-D03


title: Oligo-P02-D04


title: Oligo-P02-D01


title: Oligo-P02-F05


title: Oligo-P02-C11


title: Oligo-P02-C12


title: Oligo-P02-C10


title: Oligo-P02-E07


title: Oligo-P02-C08


title: Oligo-P02-C02


title: Oligo-P02-C01


title: Oligo-P02-E01


title: Oligo-P02-C03


title: Oligo-P02-C05


title: Oligo-P02-B06


title: Oligo-P02-B07


title: Oligo-P02-C06


title: Oligo-P02-B04


title: Oligo-P02-B12


title: Oligo-P02-B11


title: Oligo-P02-B05


title: Oligo-P02-B02


title: Oligo-P02-A12


title: Oligo-P02-A10


title: Oligo-P02-D02


title: Oligo-P02-A08


title: Oligo-P02-A05


title: Oligo-P02-A04


title: Oligo-P02-B10


title: Oligo-P02-A03


title: Oligo-P02-A02


title: Oligo-P02-A09


title: Oligo-P02-A01


title: Oligo-P02-C04


title: BCH869_GF-P01-H12

source_name: Glioma single cell


title: BCH869_GF-P01-H10


title: BCH869_GF-P01-H09


title: BCH869_GF-P01-H08


title: BCH869_GF-P01-H07


title: BCH869_GF-P01-H06


title: BCH869_GF-P01-H05


title: BCH869_GF-P01-H04


title: BCH869_GF-P01-H03


title: BCH869_GF-P01-H02


title: BCH869_GF-P01-G10


title: BCH869_GF-P01-G12


title: BCH869_GF-P01-G11


title: BCH869_GF-P01-G07


title: BCH869_GF-P01-G08


title: BCH869_GF-P01-G09


title: Oligo-P02-A07


title: BCH869_GF-P01-G05


title: BCH869_GF-P01-G06


title: BCH869_GF-P01-G03


title: BCH869_GF-P01-G01


title: BCH869_GF-P01-G02


title: BCH869_GF-P01-G04


title: BCH869_GF-P01-F10


title: BCH869_GF-P01-F11


title: BCH869_GF-P01-F05


title: BCH869_GF-P01-F08


title: BCH869_GF-P01-F07


title: BCH869_GF-P01-F06


title: BCH869_GF-P01-F09


title: BCH869_GF-P01-F03


title: BCH869_GF-P01-F02


title: BCH869_GF-P01-F01


title: BCH869_GF-P01-E12


title: BCH869_GF-P01-E10


title: BCH869_GF-P01-E07


title: BCH869_GF-P01-E09


title: BCH869_GF-P01-E06


title: BCH869_GF-P01-E05


title: BCH869_GF-P01-E04


title: BCH869_GF-P01-D11


title: BCH869_GF-P01-E03


title: BCH869_GF-P01-D10


title: BCH869_GF-P01-D09


title: BCH869_GF-P01-D07


title: BCH869_GF-P01-D05


title: BCH869_GF-P01-D04


title: BCH869_GF-P01-D02


title: BCH869_GF-P01-D01


title: BCH869_GF-P01-C10


title: BCH869_GF-P01-C06


title: BCH869_GF-P01-C05


title: BCH869_GF-P01-F04


title: BCH869_GF-P01-D06


title: BCH869_GF-P01-C04


title: BCH869_GF-P01-C08


title: BCH869_GF-P01-C07


title: BCH869_GF-P01-C01


title: BCH869_GF-P01-B07


title: BCH869_GF-P01-C09


title: BCH869_GF-P01-C11


title: BCH869_GF-P01-B04


title: BCH869_GF-P01-C03


title: BCH869_GF-P01-B01


title: BCH869_SF-P01-H12


title: BCH869_SF-P01-H11


title: BCH869_GF-P01-C02


title: BCH869_GF-P01-D08


title: BCH869_GF-P01-D03


title: BCH869_SF-P01-H07


title: BCH869_SF-P01-H08


title: BCH869_SF-P01-G10


title: BCH869_SF-P01-G12


title: BCH869_SF-P01-H01


title: BCH869_SF-P01-H06


title: BCH869_SF-P01-H02


title: BCH869_SF-P01-G08


title: BCH869_GF-P01-B06


title: BCH869_SF-P01-G06


title: BCH869_SF-P01-G04


title: BCH869_SF-P01-G09


title: BCH869_SF-P01-G07


title: BCH869_GF-P01-B03


title: BCH869_SF-P01-G03


title: BCH869_SF-P01-H10


title: BCH869_SF-P01-G02


title: BCH869_SF-P01-G01


title: BCH869_SF-P01-F11


title: BCH869_SF-P01-F12


title: BCH869_SF-P01-F10


title: BCH869_SF-P01-F09


title: BCH869_SF-P01-F04


title: BCH869_SF-P01-H09


title: BCH869_SF-P01-F01


title: BCH869_SF-P01-F02


title: BCH869_SF-P01-E11


title: BCH869_SF-P01-F03


title: BCH869_SF-P01-E10


title: BCH869_SF-P01-G11


title: BCH869_SF-P01-E08


title: BCH869_SF-P01-E07


title: BCH869_SF-P01-E02


title: BCH869_SF-P01-E01


title: BCH869_SF-P01-E03


title: BCH869_SF-P01-D12


title: BCH869_SF-P01-D10


title: BCH869_SF-P01-E06


title: BCH869_SF-P01-D11


title: BCH869_SF-P01-E04


title: BCH869_SF-P01-D08


title: BCH869_SF-P01-D09


title: BCH869_SF-P01-F08


title: BCH869_SF-P01-D07


title: BCH869_SF-P01-D04


title: BCH869_SF-P01-C12


title: BCH869_SF-P01-D01


title: BCH869_SF-P01-C07


title: BCH869_SF-P01-C08


title: BCH869_SF-P01-C09


title: BCH869_SF-P01-C03


title: BCH869_SF-P01-C06


title: BCH869_SF-P01-E09


title: BCH869_SF-P01-C02


title: BCH869_SF-P01-C01


title: BCH869_SF-P01-B12


title: BCH869_SF-P01-B10


title: BCH869_SF-P01-B02


title: BCH869_SF-P01-B09


title: BCH869_SF-P01-D06


title: BCH869_SF-P01-B11


title: BCH869_SF-P01-B03


title: BCH869_SF-P01-B08


title: BCH869_SF-P01-A12


title: BCH869_SF-P01-B05


title: BCH869_SF-P01-B01


title: BCH869_SF-P01-A10


title: BCH869_SF-P01-D03


title: BCH869_SF-P01-B04


title: BCH869_SF-P01-C10


title: BCH869_SF-P01-A11


title: BCH869_SF-P01-A06


title: BCH869_SF-P01-A09


title: BCH869_SF-P01-A03


title: BCH869_SF-P01-A04


title: BCH869_SF-P01-A02


title: BCH869_SF-P01-A05


title: BCH869_SF-P01-A08


title: BCH869_SF-P01-A01


title: BCH869_DGC100-P01-H12


title: BCH869_SF-P01-B06


title: BCH869_DGC100-P01-H11


title: BCH869_DGC100-P01-H09


title: BCH869_SF-P01-B07


title: BCH869_DGC100-P01-H06


title: BCH869_DGC100-P01-H05


title: BCH869_DGC100-P01-H02


title: BCH869_DGC100-P01-H08


title: BCH869_DGC100-P01-H04


title: BCH869_DGC100-P01-H01


title: BCH869_DGC100-P01-G10


title: BCH869_SF-P01-A07


title: BCH869_DGC100-P01-G09


title: BCH869_DGC100-P01-G11


title: BCH869_DGC100-P01-G07


title: BCH869_DGC100-P01-G12


title: BCH869_DGC100-P01-G08


title: BCH869_DGC100-P01-H10


title: BCH869_DGC100-P01-G03


title: BCH869_DGC100-P01-F11


title: BCH869_DGC100-P01-F12


title: BCH869_DGC100-P01-G01


title: BCH869_DGC100-P01-G05


title: BCH869_DGC100-P01-G06


title: BCH869_DGC100-P01-H07


title: BCH869_DGC100-P01-F10


title: BCH869_DGC100-P01-G04


title: BCH869_DGC100-P01-F09


title: BCH869_DGC100-P01-F08


title: BCH869_SF-P01-C11


title: BCH869_SF-P01-D02


title: BCH869_DGC100-P01-F06


title: BCH869_DGC100-P01-F01


title: BCH869_DGC100-P01-F03


title: BCH869_DGC100-P01-F04


title: BCH869_DGC100-P01-F02


title: BCH869_DGC100-P01-F05


title: BCH869_DGC100-P01-E10


title: BCH869_DGC100-P01-E06


title: BCH869_DGC100-P01-E05


title: BCH869_DGC100-P01-E12


title: BCH869_DGC100-P01-E11


title: BCH869_DGC100-P01-E04


title: BCH869_DGC100-P01-E01


title: BCH869_DGC100-P01-E08


title: BCH869_DGC100-P01-D12


title: BCH869_DGC100-P01-E03


title: BCH869_DGC100-P01-E02


title: BCH869_DGC100-P01-D09


title: BCH869_DGC100-P01-D10


title: BCH869_DGC100-P01-D06


title: BCH869_DGC100-P01-D05


title: BCH869_DGC100-P01-D07


title: BCH869_DGC100-P01-D08


title: BCH869_DGC100-P01-D11


title: BCH869_DGC100-P01-D03


title: BCH869_DGC100-P01-D04


title: BCH869_DGC100-P01-D02


title: BCH869_DGC100-P01-D01


title: BCH869_DGC100-P01-C12


title: BCH869_DGC100-P01-C07


title: BCH869_DGC100-P01-C08


title: BCH869_DGC100-P01-C09


title: BCH869_DGC100-P01-C10


title: BCH869_DGC100-P01-C03


title: BCH869_DGC100-P01-C04


title: BCH869_DGC100-P01-C05


title: BCH869_DGC100-P01-C06


title: BCH869_DGC100-P01-C01


title: BCH869_DGC100-P01-B11


title: BCH869_DGC100-P01-C02


title: BCH869_DGC100-P01-B04


title: BCH869_DGC100-P01-B09


title: BCH869_DGC100-P01-B06


title: BCH869_DGC100-P01-A10


title: BCH869_DGC100-P01-A11


title: BCH869_DGC100-P01-B03


title: BCH869_DGC100-P01-A12


title: BCH869_DGC100-P01-C11


title: BCH869_DGC100-P01-B02


title: BCH869_DGC100-P01-A06


title: BCH869_DGC100-P01-A08


title: BCH869_DGC100-P01-A07


title: BCH869_DGC100-P01-B01


title: BCH869_DGC100-P01-A05


title: BCH869_DGC100-P01-A04


title: BCH869_DGC100-P01-A03


title: BCH869_DGC100-P01-B08


title: BCH869_DGC100-P01-A01


title: BCH869_DGC75-P03-H11


title: BCH869_DGC75-P03-H09


title: BCH869_DGC75-P03-H07


title: BCH869_DGC75-P03-H10


title: BCH869_DGC75-P03-H06


title: BCH869_DGC100-P01-B05


title: BCH869_DGC100-P01-B10


title: BCH869_DGC100-P01-A09


title: BCH869_DGC75-P03-H03


title: BCH869_DGC75-P03-H05


title: BCH869_DGC75-P03-H02


title: BCH869_DGC75-P03-H01


title: BCH869_DGC75-P03-G11


title: BCH869_DGC75-P03-G09


title: BCH869_DGC75-P03-G08


title: BCH869_DGC75-P03-G12


title: BCH869_DGC75-P03-G06


title: BCH869_DGC75-P03-G05


title: BCH869_DGC75-P03-G04


title: BCH869_DGC75-P03-G03


title: BCH869_DGC100-P01-A02


title: BCH869_DGC75-P03-H12


title: BCH869_DGC75-P03-G02


title: BCH869_DGC75-P03-G01


title: BCH869_DGC75-P03-F12


title: BCH869_DGC75-P03-H08


title: BCH869_DGC75-P03-F11


title: BCH869_DGC75-P03-F10


title: BCH869_DGC75-P03-F07


title: BCH869_DGC75-P03-F08


title: BCH869_DGC75-P03-F01


title: BCH869_DGC75-P03-F03


title: BCH869_DGC75-P03-F05


title: BCH869_DGC75-P03-H04


title: BCH869_DGC75-P03-F06


title: BCH869_DGC75-P03-F02


title: BCH869_DGC75-P03-E12


title: BCH869_DGC75-P03-E07


title: BCH869_DGC75-P03-E09


title: BCH869_DGC75-P03-E11


title: BCH869_DGC75-P03-E06


title: BCH869_DGC75-P03-E03


title: BCH869_DGC75-P03-E08


title: BCH869_DGC75-P03-E05


title: BCH869_DGC75-P03-E02


title: BCH869_DGC75-P03-E01


title: BCH869_DGC75-P03-D12


title: BCH869_DGC75-P03-D10


title: BCH869_DGC75-P03-D07


title: BCH869_DGC75-P03-D05


title: BCH869_DGC75-P03-D09


title: BCH869_DGC75-P03-D06


title: BCH869_DGC75-P03-D11


title: BCH869_DGC75-P03-F04


title: BCH869_DGC75-P03-D03


title: BCH869_DGC75-P03-D04


title: BCH869_DGC75-P03-D02


title: BCH869_DGC75-P03-C12


title: BCH869_DGC75-P03-C09


title: BCH869_DGC75-P03-C11


title: BCH869_DGC75-P03-E10


title: BCH869_DGC75-P03-C05


title: BCH869_DGC75-P03-C07


title: BCH869_DGC75-P03-C03


title: BCH869_DGC75-P03-E04


title: BCH869_DGC75-P03-C01


title: BCH869_DGC75-P03-C02


title: BCH869_DGC75-P03-C04


title: BCH869_DGC75-P03-B10


title: BCH869_DGC75-P03-B09


title: BCH869_DGC75-P03-B06


title: BCH869_DGC75-P03-B03


title: BCH869_DGC75-P03-B04


title: BCH869_DGC75-P03-B05


title: BCH869_DGC75-P03-B01


title: BCH869_DGC75-P03-A04


title: BCH869_DGC75-P03-A05


title: BCH869_DGC75-P03-A07


title: BCH869_DGC75-P02-H12


title: BCH869_DGC75-P03-C10


title: BCH869_DGC75-P03-A02


title: BCH869_DGC75-P03-A01


title: BCH869_DGC75-P02-H07


title: BCH869_DGC75-P02-H10


title: BCH869_DGC75-P03-B07


title: BCH869_DGC75-P02-H02


title: BCH869_DGC75-P02-G12


title: BCH869_DGC75-P02-G10


title: BCH869_DGC75-P02-H01


title: BCH869_DGC75-P02-G09


title: BCH869_DGC75-P03-B02


title: BCH869_DGC75-P02-H09


title: BCH869_DGC75-P02-H04


title: BCH869_DGC75-P02-G07


title: BCH869_DGC75-P02-G06


title: BCH869_DGC75-P02-G04


title: BCH869_DGC75-P02-G05


title: BCH869_DGC75-P02-G03


title: BCH869_DGC75-P02-G01


title: BCH869_DGC75-P02-G02


title: BCH869_DGC75-P02-F11


title: BCH869_DGC75-P02-F12


title: BCH869_DGC75-P02-F10


title: BCH869_DGC75-P02-F07


title: BCH869_DGC75-P02-F06


title: BCH869_DGC75-P02-F05


title: BCH869_DGC75-P02-F04


title: BCH869_DGC75-P02-F09


title: BCH869_DGC75-P02-F02


title: BCH869_DGC75-P02-G08


title: BCH869_DGC75-P02-E10


title: BCH869_DGC75-P02-F01


title: BCH869_DGC75-P02-E09


title: BCH869_DGC75-P02-E04


title: BCH869_DGC75-P02-E05


title: BCH869_DGC75-P02-E08


title: BCH869_DGC75-P02-E07


title: BCH869_DGC75-P02-E06


title: BCH869_DGC75-P02-E01


title: BCH869_DGC75-P02-D12


title: BCH869_DGC75-P02-E02


title: BCH869_DGC75-P02-D07


title: BCH869_DGC75-P02-D10


title: BCH869_DGC75-P02-D09


title: BCH869_DGC75-P02-D08


title: BCH869_DGC75-P02-D05


title: BCH869_DGC75-P02-F03


title: BCH869_DGC75-P02-D03


title: BCH869_DGC75-P02-D04


title: BCH869_DGC75-P02-D01


title: BCH869_DGC75-P02-C11


title: BCH869_DGC75-P02-C12


title: BCH869_DGC75-P02-D02


title: BCH869_DGC75-P02-C10


title: BCH869_DGC75-P02-C08


title: BCH869_DGC75-P02-C06


title: BCH869_DGC75-P02-C07


title: BCH869_DGC75-P02-C05


title: BCH869_DGC75-P02-D11


title: BCH869_DGC75-P02-C04


title: BCH869_DGC75-P02-C02


title: BCH869_DGC75-P02-C03


title: BCH869_DGC75-P02-B12


title: BCH869_DGC75-P02-B09


title: BCH869_DGC75-P02-B11


title: BCH869_DGC75-P02-B10


title: BCH869_DGC75-P02-D06


title: BCH869_DGC75-P02-B07


title: BCH869_DGC75-P02-B08


title: BCH869_DGC75-P02-B03


title: BCH869_DGC75-P02-B05


title: BCH869_DGC75-P02-B02


title: BCH869_DGC75-P02-B01


title: BCH869_DGC75-P02-A11


title: BCH869_DGC75-P02-C09


title: BCH869_DGC75-P02-A09


title: BCH869_DGC75-P02-A10


title: BCH869_DGC75-P02-A08


title: BCH869_DGC75-P02-A07


title: BCH869_DGC75-P02-A06


title: BCH869_DGC75-P02-A05


title: BCH869_DGC75-P02-A03


title: BCH869_DGC75-P02-A04


title: BCH869_DGC75-P02-C01


title: BCH869_DGC75-P02-A01


title: BCH869_DGC75-P02-B06


title: BCH869_GS-P06-H11


title: BCH869_GS-P06-H12


title: BCH869_DGC75-P02-A02


title: BCH869_GS-P06-H08


title: BCH869_GS-P06-H04


title: BCH869_GS-P06-H06


title: BCH869_GS-P06-H03


title: BCH869_GS-P06-G12


title: BCH869_DGC75-P02-A12


title: BCH869_DGC75-P02-G11


title: BCH869_GS-P06-G11


title: BCH869_GS-P06-H09


title: BCH869_GS-P06-G06


title: BCH869_GS-P06-G04


title: BCH869_GS-P06-G05


title: BCH869_GS-P06-G08


title: BCH869_GS-P06-G02


title: BCH869_GS-P06-G03


title: BCH869_GS-P06-G01


title: BCH869_GS-P06-F12


title: BCH869_GS-P06-F10


title: BCH869_GS-P06-F09


title: BCH869_GS-P06-F11


title: BCH869_GS-P06-F08


title: BCH869_GS-P06-F07


title: BCH869_GS-P06-F06


title: BCH869_GS-P06-H07


title: BCH869_GS-P06-F02


title: BCH869_GS-P06-H01


title: BCH869_GS-P06-F04


title: BCH869_GS-P06-G07


title: BCH869_GS-P06-E11


title: BCH869_GS-P06-E09


title: BCH869_GS-P06-F01


title: BCH869_GS-P06-E10


title: BCH869_GS-P06-E05


title: BCH869_GS-P06-E06


title: BCH869_GS-P06-E08


title: BCH869_GS-P06-E07


title: BCH869_GS-P06-E04


title: BCH869_GS-P06-F05


title: BCH869_GS-P06-D12


title: BCH869_GS-P06-E03


title: BCH869_GS-P06-E02


title: BCH869_GS-P06-D09


title: BCH869_GS-P06-D11


title: BCH869_GS-P06-D08


title: BCH869_GS-P06-D06


title: BCH869_GS-P06-D04


title: BCH869_GS-P06-D03


title: BCH869_GS-P06-D02


title: BCH869_GS-P06-C11


title: BCH869_GS-P06-C10


title: BCH869_GS-P06-C09


title: BCH869_GS-P06-C07


title: BCH869_GS-P06-C08


title: BCH869_GS-P06-C04


title: BCH869_GS-P06-C06


title: BCH869_GS-P06-C03


title: BCH869_GS-P06-C02


title: BCH869_GS-P06-B09


title: BCH869_GS-P06-B10


title: BCH869_GS-P06-B08


title: BCH869_GS-P06-D10


title: BCH869_GS-P06-B06


title: BCH869_GS-P06-D07


title: BCH869_GS-P06-B05


title: BCH869_GS-P06-B02


title: BCH869_GS-P06-B03


title: BCH869_GS-P06-A11


title: BCH869_GS-P06-A10


title: BCH869_GS-P06-A07


title: BCH869_GS-P06-D01


title: BCH869_GS-P06-A09


title: BCH869_GS-P06-A06


title: BCH869_GS-P06-A08


title: BCH869_GS-P06-A05


title: BCH869_GS-P06-A02


title: BCH869_GS-P06-A04


title: BCH869_GS-P06-C01


title: BCH869_GS-P06-B12


title: BCH869_GS-P06-B11


title: BCH869_GS-P06-A01


title: BCH869_GS-P05-H09


title: BCH869_GS-P05-H12


title: BCH869_GS-P05-H07


title: BCH869_GS-P05-H08


title: BCH869_GS-P05-H04


title: BCH869_GS-P05-H06


title: BCH869_GS-P05-H02


title: BCH869_GS-P05-H01


title: BCH869_GS-P05-H03


title: BCH869_GS-P05-H05


title: BCH869_GS-P05-G11


title: BCH869_GS-P05-G12


title: BCH869_GS-P05-G03


title: BCH869_GS-P05-G05


title: BCH869_GS-P05-G10


title: BCH869_GS-P05-G07


title: BCH869_GS-P05-F09


title: BCH869_GS-P05-G09


title: BCH869_GS-P05-F07


title: BCH869_GS-P05-F05


title: BCH869_GS-P05-F10


title: BCH869_GS-P05-G01


title: BCH869_GS-P05-G06


title: BCH869_GS-P05-F06


title: BCH869_GS-P05-F03


title: BCH869_GS-P05-F04


title: BCH869_GS-P05-F02


title: BCH869_GS-P05-F01


title: BCH869_GS-P05-E12


title: BCH869_GS-P05-E10


title: BCH869_GS-P05-E11


title: BCH869_GS-P05-E09


title: BCH869_GS-P05-E08


title: BCH869_GS-P05-E06


title: BCH869_GS-P05-E03


title: BCH869_GS-P05-D11


title: BCH869_GS-P05-D10


title: BCH869_GS-P05-D12


title: BCH869_GS-P05-D09


title: BCH869_GS-P05-E05


title: BCH869_GS-P05-D06


title: BCH869_GS-P05-D04


title: BCH869_GS-P05-D01


title: BCH869_GS-P05-C11


title: BCH869_GS-P05-C09


title: BCH869_GS-P05-D02


title: BCH869_GS-P05-D05


title: BCH869_GS-P05-D03


title: BCH869_GS-P05-C05


title: BCH869_GS-P05-C06


title: BCH869_GS-P05-C08


title: BCH869_GS-P05-C10


title: BCH869_GS-P05-C04


title: BCH869_GS-P05-C07


title: BCH869_GS-P05-C03


title: BCH869_GS-P05-C01


title: BCH869_GS-P05-C02


title: BCH869_GS-P05-B11


title: BCH869_GS-P05-B10


title: BCH869_GS-P05-B08


title: BCH869_GS-P05-B06


title: BCH869_GS-P05-B07


title: BCH869_GS-P05-B05


title: BCH869_GS-P05-B02


title: BCH869_GS-P05-A10


title: BCH869_GS-P05-A09


title: BCH869_GS-P05-A11


title: BCH869_GS-P05-A08


title: BCH869_GS-P05-C12


title: BCH869_GS-P05-A01


title: BCH869_GS-P03-H12


title: BCH869_GS-P03-H08


title: BCH869_GS-P03-H07


title: BCH869_GS-P03-H06


title: BCH869_GS-P03-H02


title: BCH869_GS-P03-H03


title: BCH869_GS-P03-G11


title: BCH869_GS-P03-G09


title: BCH869_GS-P03-G07


title: BCH869_GS-P03-G06


title: BCH869_GS-P03-H04


title: BCH869_GS-P03-G05


title: BCH869_GS-P05-B04


title: BCH869_GS-P03-G03


title: BCH869_GS-P03-G04


title: BCH869_GS-P03-F12


title: BCH869_GS-P03-F10


title: BCH869_GS-P03-F06


title: BCH869_GS-P05-A07


title: BCH869_GS-P03-G02


title: BCH869_GS-P03-F05


title: BCH869_GS-P05-A04


title: BCH869_GS-P05-A03


title: BCH869_GS-P03-F03


title: BCH869_GS-P03-H01


title: BCH869_GS-P03-E10


title: BCH869_GS-P03-E11


title: BCH869_GS-P03-G10


title: BCH869_GS-P03-F02


title: BCH869_GS-P03-E08


title: BCH869_GS-P03-E09


title: BCH869_GS-P03-D12


title: BCH869_GS-P03-D10


title: BCH869_GS-P03-E07


title: BCH869_GS-P03-E02


title: BCH869_GS-P03-E06


title: BCH869_GS-P03-D11


title: BCH869_GS-P03-D08


title: BCH869_GS-P03-D07


title: BCH869_GS-P03-D05


title: BCH869_GS-P03-D03


title: BCH869_GS-P03-C12


title: BCH869_GS-P03-D06