title: MEL06_T0_1c CTCTCTAC-GCGTAAGA

status: Public on Jul 18 2018

city: Leuven

first: Sara

last: Aibar

address: Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

description: dsRed positive single cells (tumours) were sorted into 2.5μL of RLT plus buffer (Qiagen 1053393), snap frozen on dry ice and stored at -80°C. Subsequently, the single cells’ DNA was purified and amplified using Picoplex (Rubicon R30050) following established (Macaulay et al., 2015; Macaulay et al., 2016). The amplified DNA was purified using 0.8x ratio of AMPure XP beads using a Hamilton robot and subsequently quantified using a QuantiFluor dsDNA System (Promega E2670). 100pg of amplified DNA was used to prepare Illumina sequencing libraries using a Nextera XT DNA sample preparation kit (Illumina FC-131-1096) with volumes reduced by one-tenth on a Labcyte Echo 525 liquid handling robot (Labcyte). After PCR, all samples were pooled and purified using AMPure XP beads at a 0.6x ratio. Library pools were eluted in buffer EB and quality control performed using an Agilent 2100 BioAnalyser and High Sensitivity DNA chip before adjusting to a concentration of 4nM. The diluted pools were quantified using a KAPA qPCR library quantification kit 480 (Roche 7960140001) on a LightCycler 480 before a final dilution to 1.5nM. Sequencing was performed on HiSeq4000 with 50bp single-end reads.

data_processing:
PicoPLEX_WGA
Adapter trimming using cutadapt (v 1.13)
Reads aligned to GRCh37 sequences using bwa mem (0.7.1)
LogR values were calculated for genomic bins of 500,000 uniquely mappable positions, maintaining unique reads with a minimum mapping quality of 30 (Baslan et al., 2012; Moller et al., 2013). A value of 1 was added to each bin’s single-cell read count and bins with a %GC content less than 28% were discarded. The bin counts were then transformed by taking the log2 ratio (logR) per bin by dividing the read count of a given bin by the median read count of the bins genome-wide. LogR values were corrected for GC bias using a Loess fit and normalized to the median of the genome-wide logR value. The normalised LogR values were finally segmented using piecewise constant fitting (with the penalty parameter γ set to 15).
GRCh37
tab-delimited matrix containing normalised, GC corrected read counts per bin

source_name: T0 melanoma cell

extract_protocol:
Mice with tumors reaching 1000 mm³ were started on the BRAF-MEK combination via daily oral gavage (Instech Laboratories). BRAF inhibitor dabrafenib (Tafinlar capsules) and MEK inhibitor trametinib (MCE) were dissolved in DMSO at a concentration of 30 and 0.3 mg/mL respectively, aliquoted and stored at -80°C. Each day 900 μL PBS (Sigma) was added to a new aliquot. Mice were treated with a capped dose of 600 – 6 μg dabrafenib – trametinib respectively in 200 μL total volume.
This tumor was minced followed by dissociation using collagenase I & IV (Sigma) and trypsin (Life Technologies). Cells were resuspended in serum-free DMEM/F12 medium (Thermo Fisher Scientific) and 250 000 cells were injected in the interscapular fat pad of 8 – 16 week old female NMRI nude mice (Taconic).

treatment_protocol: Fresh tumor tissue was collected in transport medium (RPMI1640 medium supplemented with 1% penicillin/streptomycin, 1 μg/mL amphotericin B and 50 μg/mL gentamicin; all from Thermo Fisher Scientific). Tumor fragments were subsequently rinsed in phosphate-buffered saline (PBS; Thermo Fisher Scientific) supplemented with penicillin/streptomycin and amphotericin B and cut into small pieces of approximately 3 x 3 x 3 mm3. Tumor pieces were implanted subcutaneously in the intercapsular fat pad of female SCID-beige mice (Taconic)

tag: tissue

value: tumor (PDX MEL006)

value: before treatment

tag: genotype

value: BRAFmut (V600E)


title: MEL06_T0_1c ATCTCAGG-TTATGCGA

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: age


title: MEL06_T0_1c TAGCGCTC-TTATGCGA


title: MEL06_T0_1c ACTGAGCG-TTATGCGA


title: MEL06_T0_50c TAAGGCGA-TCGACTAG

source_name: T0 50melanoma cells


title: MEL06_T0_50c TCGACGTC-TTATGCGA


title: MEL06_T0_1c CGTACTAG-GAGCCTTA


title: MEL06_T0_1c GCTCATGA-CTATTAAG


title: MEL06_T0_1c ATGCGCAG-TTATGCGA


title: MEL06_T0_1c CGATCAGT-TTATGCGA


title: Uhordei_axenicCulture_R1

status: Public on Jul 19 2018

type: RNA

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

country: Germany

institute: Fraunhofer ITEM

hyb_protocol: Samples for Microarray analyses were processed with Gene Expression Hybridization Kit, Gene Expression Wash Buffer Kit (Agilent) and the RNeasy Mini Kit (Qiagen) according to the manufacturers’ instructions.

scan_protocol: Total-RNA was used as input for reverse transcription.Microarrays were performed on 8x15k microarrays (Agilent) and scanned using the following parameters: profile: AgilentHD_GX_1Color,Slide ID: AutoDetect, Channels: G, Scan region: Agilent HD (61 x 21,6mm), resolution: 2µm, Tiff: 20bit, RPMT: 100%, GPMT: 100%, XDS: no XDR. The image was processed in Agilent Feature Extraction and data analysis was performed using Partek® Genomics Suite Software (Partek Inc.).

data_processing: Changes in U. hordei gene expression in planta (at 20 hpi, 40 hpi, 3 dpi and 6 dpi) were calculated relative to U. hordei yeast-like cells grown in axenic culture.

molecule: total RNA

organism: Ustilago hordei

source_name: U. hordei cells in axenic culture

label_protocol: Samples for Microarray analyses were processed with the One Color Quick Amp Labeling kit, One Color Spike-In Kit, (Agilent)

growth_protocol: Ustilago hordei (4857-4 Mat-1 and 4857-5 Mat-2) cultures were incubated in YEPSlight (0.4% yeast extract, 0.4% peptone, and 2% saccharose) liquid medium at 22°C with 200 rpm shaking. Susceptible barley cultivar (Golden Promise) was grown in a greenhouse at 70% relative humidity, at 22°C during the day and the night; with a light/dark regime of 15/9 hrs and 100 Watt m-2 supplemental light when the sunlight influx intensity was less than 150 Watt m-2.

extract_protocol: Total RNA was isolated from axenic culture and U. hordei-infected barley plants (at 20 hpi, 40 hpi, 3 dpi and 6 dpi). The third leaf of the infected barley plant was collected by cutting 1 cm below the injection needle sites and approximately 3 cm of the leaf was taken for RNA extraction. For 20 hpi time point the melted latex was used to collect penetrated fungal materials. Samples were then frozen in liquid nitrogen and grinded by using a mortar and pestle under constant liquid nitrogen cooling conditions. The total RNA was isolated from the fine powder using the TRIzol® extraction method (Invitrogen; Karlsruhe, Germany) according to the manufacturer’s instructions. Total RNA was then cleaned with Turbo DNA-Free™ Kit (Ambion/Applied Biosystems; Darmstadt, Germany) to remove any DNA contamination according to the manufacturer’s instructions.

treatment_protocol: For virulence assay, both wild type and mutant strains of U. hordei were grown in YEPSlight liquid medium at 22°C and 200 rpm shaking to get an OD600 of 0.6-0.8. The cells were then centrifuged at 3500 rpm for 10 min at RT and resuspended in sterile water supplemented with 0.1% Tween-20 to get the OD600 of 3.0. Then U. hordei suspension was injected into the center of the leaf whirl of 10 to 12-day-old barley seedlings (three-leaf stage) with a syringe with needle. All infection assays were performed in three biological replicates with at least 16 plants.

tag: growth condition

value: Axenic culture

tag: dpi

value: Axenic culture OD:1


title: Uhordei_infectedBarleySeedling_20hpi_R1

source_name: U. hordei infected barley seedling at 20 hpi

value: in planta

value: at 20 hpi on barley


title: Uhordei_infectedBarleySeedling_20hpi_R2


title: Uhordei_axenicCulture_R2


title: MEL06_T0_1c GGAGCTAC-TTATGCGA


title: Uhordei_axenicCulture_R3


title: MEL06_T0_1c TGCAGCTA-TTATGCGA


title: fetal BMPR1B NEG 2

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

country: USA

institute: University of Southern  California

description:
Fetal_BMPR1B_Neg_cartilage_sample2
14_ATTCCT_L001

library_source: transcriptomic

data_processing:
Reads were mapped to the human genome (hg19) using RefSeq annotation
Transcript estimation was performed using RNA-Seq by Expectation Maximization method (Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics. 2011;12(323)
Differenential expression was performed using the EBSeq method (Leng N, Dawson JA, Thomson JA, et al. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics. 2013;29(8):1035-1043.)
Genome_build: hg19

source_name: fetal BMPR1B NEG

extract_protocol:
Qiagen Micro kit
Library preparation with Kapa mRNA-Seq kit

tag: developmental stage

value: 17 wks

value: Knee


title: fetal BMPR1B NEG 1

description:
Fetal_BMPR1B_Neg_cartilage_sample1
10_GTTTCG_L001


title: fetal BMPR1B NEG 4

description:
Fetal_BMPR1B_Neg_cartilage_sample4
22_GTTTCG_L002


title: envz600

city: Hefei

first: Zhi

last: Liang

address: No.96, JinZhai Road

department: School of Life Sciences

country: China

institute: University of Science & Technology of C

description: Wildtype

data_processing:
Sequencing reads were mapped to the E. coli genome with bowtie2
Read counts per gene determined using HTseq count before normalized using DESeq2
PCA analysis was performed using the top 500 genes with the most variations.
Supplementary_files_format_and_content: The txt file includes the gene expression profiles of all the samples. The xlsx file contains the PC1 and PC2 values of all the samples.

organism: Escherichia coli

growth_protocol: Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight.

extract_protocol:
After exposed under the red light with a specific ON/OFF frequency for 10 hours, 1ml bacterial culture was sampled and the bacterial cells were collected at 4 °C. The total RNA of E. coli was extracted using RNAprep pure Cell/Bacteria Kit (TIANGEN, DP430) and preserved at -80 °C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In the 15 ml centrifuge tube (Corning, 430791), the overnight culture was diluted to 2ml in fresh LB medium containing Ampicillin (50 ng/μl), Chloramphenicol (170 ng/μl) and IPTG (0.5mM) to reach OD600 = 0.01. The LED tube was screwed into the centrifuge tube and connected with the control box. Then the power of the control box was turned on and the LED frequency input was generated. At last, the 15 ml centrifuge tube with LED tube was put into the Thermomixer comfort (Eppendorf) and shaken at 650 rpm and 37°C for 10 hours.

tag: plasmid

value: pLCenvZ, pPCB (wild type)

tag: strain

tag: input signal frequency


title: MEL06_T0_1c CCTAAGAC-TTATGCGA


title: MEL06_T0_1c TACGCTGC-TTATGCGA


title: MEL06_T0_1c GCGTAGTA-TTATGCGA


title: FPS1: wt_R1

city: La Jolla

first: Adam

middle: M

last: Feist

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California, San Diego

data_processing:
Sequenced reads were mapped onto CP009273.1 reference genome sequence using bowtie2 v.2.3.4.1 with parameters -X 1000 -N 1 -p 20 -3 3 -1 <R1_files> -2 <R2_files> -x <index>.
The SAM output file of bowtie2 was converted to BAM and sorted using samtools version 1.8
Expression levels of each gene in units transcripts per million (TPM) were computed from fragment counts normalized per kilobase of feature length per million mapped fragments (FPKM) using the R (v.3.5.0) package DESeq2 in Bioconductor.
Differentially expressed genes were identified using the R package DESeq2 in Bioconductor. Gene expression fold changes were considered significant if the log2(fold change) was greater than 1 and the calculated p-value was smaller that 0.05.
Genome_build: CP009273.1
Supplementary_files_format_and_content: A single .csv file containing all TPM values in a matrix table for all genes in each sample is provided.

organism: Escherichia coli BW25113

source_name: wild type

growth_protocol: All samples were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 2 g/L D-glucose and 50 mg/L Kanamycin A (with the exception of wild type which was grown in the absence of antibiotics) .

extract_protocol:
Total RNA was isolated and purified using Qiagen’s RNeasy minikit column according to the manufacturer’s specifications. The total RNA quality was checked with the Agilent Bioanalyzer RNA 600 nano kit. Ribosomal RNA (rRNA) was removed utilizing Ribo-Zero rRNA removal kit (Epicentre) for Gram-negative bacteria.
The KAPA RNA HyperPrep kit (Kapa Biosystems) was used for generation of paired-end, strand-specific RNA sequencing libraries. The final pool of libraries was subjected to a 1x SPRI bead size selection to further remove unincorporated PCR primers.
RNAsequencing libraries were run on an Illumina NextSeq 550 machine using a NextSeq 500/550 Mid Output v2 kit (150 cycles).

treatment_protocol: The cell cultures were treated with RNAprotect reagent (Qiagen).

tag: carbon source

value: D-glucose

tag: genotype/variation

value: wild type


title: MEL06_T0_1c CGGAGCCT-TTATGCGA


title: MEL06_T0_1c ACTCGCTA-TTATGCGA


title: MEL06_T0_10c TCGACGTC-GAGCCTTA

source_name: T0 10melanoma cells


title: MEL06_T0_1c TGCAGCTA-GAGCCTTA


title: MEL06_T0_1c CGATCAGT-GAGCCTTA


title: MEL06_T0_1c CCTAAGAC-GAGCCTTA


title: MEL06_T0_1c ACTGAGCG-GAGCCTTA


title: D1_3

city: Fuyang

first: Mi

last: NI

state: Anhui

address: No.100 Qinghe West Road

institute: Fuyang Normal Univ

data_processing:
The original image data is transferred into sequence data via base calling
We use BWA to map clean reads to genome reference and use Bowtie to gene reference.
Genes and isoforms expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization).
Genome_build: http://genome.jgi.doe.gov/Trias1/Trias1.download.html
Supplementary_files_format_and_content: FPKM calculated using RSEM, FPKM values represent counting fragments, not reads.

organism: Trichoderma asperellum

source_name: Trichoderma_100 μg/mL  dichlorvos

growth_protocol: The spore suspension of T. asperellum TJ01 was transferred to PD medium. After culturing at 28°C and 180 rpm for 24 h

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instruction.
The mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates.

treatment_protocol: Culturing in Burk broth containing 0 μg/mL (control), 100 μg/mL, 500 μg/mL, or 1000 μg/mL dichlorvos at 28°C and 180 rpm for 24 h

tag: treated with

value: 100 μg/mL  dichlorvos at 28°C and 180 rpm for 24 h


title: MEL06_T0_1c GGAGCTAC-GAGCCTTA


title: MEL06_T0_1c ATGCGCAG-GAGCCTTA


title: MEL06_T0_1c GCGTAGTA-GAGCCTTA


title: MEL06_T0_1c TACGCTGC-GAGCCTTA


title: MEL06_T0_1c CGGAGCCT-GAGCCTTA


title: MEL06_T0_1c TGCAGCTA-AAGGCTAT


title: MEL06_T0_1c TAGCGCTC-GAGCCTTA


title: MEL06_T0_1c CGATCAGT-AAGGCTAT


title: MEL06_T0_1c ACTGAGCG-AAGGCTAT


title: MEL06_T0_1c GCGTAGTA-AAGGCTAT


title: MEL06_T0_1c ATGCGCAG-AAGGCTAT


title: MEL06_T0_1c GGAGCTAC-AAGGCTAT


title: MEL06_T0_1c TAGCGCTC-AAGGCTAT


title: MEL06_T0_1c TACGCTGC-AAGGCTAT


title: MEL06_T0_50c TCGACGTC-CTATTAAG


title: MEL06_T0_1c CGGAGCCT-AAGGCTAT


title: MEL06_T0_1c TGCAGCTA-CTATTAAG


title: MEL06_T0_1c ACTCGCTA-AAGGCTAT


title: MEL06_T0_1c ACTCGCTA-GAGCCTTA


title: MEL06_T0_1c TAGCGCTC-CTATTAAG


title: MEL06_T0_1c ATGCGCAG-CTATTAAG


title: MEL06_T0_1c ACTGAGCG-CTATTAAG


title: MEL06_T0_1c CCTAAGAC-CTATTAAG


title: MEL06_T0_1c CCTAAGAC-AAGGCTAT


title: MEL06_T0_1c ACTCGCTA-CTATTAAG


title: MEL06_T0_1c GGAGCTAC-CTATTAAG


title: MEL06_T0_1c GCGTAGTA-CTATTAAG


title: MEL06_T0_1c CGGAGCCT-CTATTAAG


title: MEL06_T0_1c CGATCAGT-GCGTAAGA


title: MEL06_T0_10c TCGACGTC-GCGTAAGA


title: MEL06_T0_1c CGATCAGT-CTATTAAG


title: MEL06_T0_1c ACTGAGCG-GCGTAAGA


title: MEL06_T0_1c CCTAAGAC-GCGTAAGA


title: MEL06_T0_1c TAGCGCTC-GCGTAAGA


title: MEL06_T0_1c ATGCGCAG-GCGTAAGA


title: MEL06_T0_1c CGGAGCCT-GCGTAAGA


title: MEL06_T0_1c GCGTAGTA-GCGTAAGA


title: MEL06_T0_1c TGCAGCTA-CCTAGAGT


title: MEL06_T0_1c TACGCTGC-CTATTAAG


title: MEL06_T0_1c ACTGAGCG-CCTAGAGT


title: MEL06_T0_1c CCTAAGAC-CCTAGAGT


title: MEL06_T0_1c TGCAGCTA-GCGTAAGA


title: MEL06_T0_1c TACGCTGC-CCTAGAGT


title: MEL06_T0_1c GGAGCTAC-CCTAGAGT


title: MEL06_T0_1c CGGAGCCT-CCTAGAGT


title: MEL06_T0_1c GCGTAGTA-CCTAGAGT


title: MEL06_T0_1c TAGCGCTC-CCTAGAGT


title: MEL06_T0_10c TCGACGTC-TTCTAGCT


title: MEL06_T0_1c ACTCGCTA-CCTAGAGT


title: MEL06_T0_1c TGCAGCTA-TTCTAGCT


title: MEL06_T0_1c CGATCAGT-TTCTAGCT


title: MEL06_T0_1c TAGCGCTC-TTCTAGCT


title: MEL06_T0_1c ACTGAGCG-TTCTAGCT


title: MEL06_T0_1c CCTAAGAC-TTCTAGCT


title: MEL06_T0_1c TACGCTGC-GCGTAAGA


title: MEL06_T0_1c TACGCTGC-TTCTAGCT


title: MEL06_T0_1c CGGAGCCT-TTCTAGCT


title: MEL06_T0_1c ACTCGCTA-TTCTAGCT


title: MEL06_T0_1c GCGTAGTA-TTCTAGCT


title: MEL06_T0_1c GGAGCTAC-TTCTAGCT


title: MEL06_T0_1c CGATCAGT-CCTAGAGT


title: MEL06_T0_1c GGAGCTAC-GCGTAAGA


title: MEL06_T0_1c TGCAGCTA-TCGACTAG


title: MEL06_T0_1c CCTAAGAC-TCGACTAG


title: MEL06_T0_1c CGATCAGT-TCGACTAG


title: MEL06_T0_1c ATGCGCAG-CCTAGAGT


title: MEL06_T0_1c ATGCGCAG-TCGACTAG


title: MEL06_T0_1c TAGCGCTC-TCGACTAG


title: MEL06_T0_1c ACTGAGCG-TCGACTAG


title: MEL06_T0_1c TACGCTGC-TCGACTAG


title: MEL06_T0_1c GCGTAGTA-TCGACTAG


title: MEL06_T0_1c ATGCGCAG-TTCTAGCT


title: MEL06_T0_1c CGGAGCCT-TCGACTAG


title: MEL06_T0_1c ACTCGCTA-TCGACTAG


title: MEL06_T28_1c TGCAGCTA-TCTCTCCG

source_name: phase2 melanoma cell

value: 28d on treatment


title: MEL06_T28_1c TCGACGTC-TCTCTCCG


title: MEL06_T28_1c CGATCAGT-TCTCTCCG


title: MEL06_T0_1c GGAGCTAC-TCGACTAG


title: MEL06_T28_1c ATGCGCAG-TCTCTCCG


title: MEL06_T28_1c GCGTAGTA-TCTCTCCG


title: MEL06_T28_1c TACGCTGC-TCTCTCCG


title: MEL06_T28_1c ACTGAGCG-TCTCTCCG


title: MEL06_T28_1c CGGAGCCT-TCTCTCCG


title: MEL06_T28_1c CCTAAGAC-TCTCTCCG


title: MEL06_T28_1c TCGACGTC-CGTCTAAT


title: MEL06_T28_1c ACTGAGCG-CGTCTAAT


title: MEL06_T28_1c TAGCGCTC-CGTCTAAT


title: MEL06_T28_1c TGCAGCTA-CGTCTAAT


title: MEL06_T28_1c CGATCAGT-CGTCTAAT


title: MEL06_T28_1c CCTAAGAC-CGTCTAAT


title: MEL06_T28_1c ATGCGCAG-CGTCTAAT


title: MEL06_T28_1c CGGAGCCT-CGTCTAAT


title: MEL06_T28_1c TCGACGTC-CTAAGCCT


title: MEL06_T28_1c TACGCTGC-CGTCTAAT


title: MEL06_T28_1c GCGTAGTA-CGTCTAAT


title: MEL06_T28_1c TAGCGCTC-TCTCTCCG


title: MEL06_T28_1c CGATCAGT-CTAAGCCT


title: MEL06_T28_1c CCTAAGAC-CTAAGCCT


title: MEL06_T28_1c ACTGAGCG-CTAAGCCT


title: MEL06_T28_1c GGAGCTAC-TCTCTCCG


title: MEL06_T28_1c TAGCGCTC-CTAAGCCT


title: MEL06_T28_1c ATGCGCAG-CTAAGCCT


title: MEL06_T28_1c GGAGCTAC-CTAAGCCT


title: MEL06_T28_1c GCGTAGTA-CTAAGCCT


title: MEL06_T28_1c TACGCTGC-CTAAGCCT


title: MEL06_T28_1c CGGAGCCT-CTAAGCCT


title: MEL06_T28_1c TCGACGTC-AAGGAGTA


title: MEL06_T28_1c GGAGCTAC-CGTCTAAT


title: MEL06_T28_1c TGCAGCTA-ACTGCATA


title: MEL06_T28_1c CGGAGCCT-AAGGAGTA


title: MEL06_T28_1c TACGCTGC-AAGGAGTA


title: MEL06_T28_1c TGCAGCTA-AAGGAGTA


title: MEL06_T28_1c CCTAAGAC-AAGGAGTA


title: MEL06_T28_1c TAGCGCTC-AAGGAGTA


title: MEL06_T28_1c CGATCAGT-ACTGCATA


title: MEL06_T28_1c ACTGAGCG-ACTGCATA


title: MEL06_T28_1c ACTGAGCG-AAGGAGTA


title: MEL06_T28_1c ATGCGCAG-ACTGCATA


title: MEL06_T28_1c TACGCTGC-ACTGCATA


title: MEL06_T28_1c TAGCGCTC-ACTGCATA


title: MEL06_T28_1c GCGTAGTA-AAGGAGTA


title: MEL06_T28_1c CGATCAGT-AAGGAGTA


title: MEL06_T28_1c CCTAAGAC-ACTGCATA


title: MEL06_T28_1c GCGTAGTA-ACTGCATA


title: MEL06_T28_1c CGGAGCCT-ACTGCATA


title: MEL06_T28_1c ATGCGCAG-AAGGAGTA


title: MEL06_T28_1c TGCAGCTA-CTAAGCCT


title: MEL06_T28_1c TGCAGCTA-GTAAGGAG


title: MEL06_T28_1c TCGACGTC-GTAAGGAG


title: MEL06_T28_1c CGATCAGT-GTAAGGAG


title: MEL06_T28_1c CCTAAGAC-GTAAGGAG


title: MEL06_T28_1c TAGCGCTC-GTAAGGAG


title: MEL06_T28_1c TACGCTGC-GTAAGGAG


title: MEL06_T28_1c ACTGAGCG-GTAAGGAG


title: MEL06_T28_1c GGAGCTAC-ACTGCATA


title: MEL06_T28_1c CGGAGCCT-GTAAGGAG


title: MEL06_T28_1c ATGCGCAG-GTAAGGAG


title: MEL06_T28_1c GCGTAGTA-GTAAGGAG


title: MEL06_T28_1c TCGACGTC-TATCCTCT


title: MEL06_T28_1c CCTAAGAC-TATCCTCT


title: MEL06_T28_1c TAGCGCTC-TATCCTCT


title: MEL06_T28_1c GGAGCTAC-GTAAGGAG


title: MEL06_T28_1c ATGCGCAG-TATCCTCT


title: MEL06_T28_1c TGCAGCTA-TATCCTCT


title: MEL06_T28_1c ACTGAGCG-TATCCTCT


title: MEL06_T28_1c TACGCTGC-TATCCTCT


title: MEL06_T28_1c GGAGCTAC-TATCCTCT


title: MEL06_T28_1c CGGAGCCT-TATCCTCT


title: MEL06_T28_1c CGATCAGT-TATCCTCT


title: MEL06_T28_1c GCGTAGTA-TATCCTCT


title: MEL06_T28_1c TCGACGTC-CTCTCTAT


title: MEL06_T28_1c ACTGAGCG-CTCTCTAT


title: MEL06_T28_1c TAGCGCTC-CTCTCTAT


title: MEL06_T28_50c ACTCGCTA-CTCTCTAT

source_name: phase2 50melanoma cells


title: MEL06_T28_1c GGAGCTAC-CTCTCTAT


title: MEL06_T28_1c CGGAGCCT-CTCTCTAT


title: MEL06_T28_1c TACGCTGC-CTCTCTAT


title: MEL06_T28_1c ATGCGCAG-CTCTCTAT


title: MEL06_T28_1c CCTAAGAC-CTCTCTAT


title: Hand>960CTG-rep2

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

data_processing:
FastQC was used to test Quality control
Paired-end reads were aligned using bowtie 2 to the dm5 genome assembly
Differential expression studies were performed between several genotypes using a specific pipeline using Deseq2
Genome_build: Dm5.49
Supplementary_files_format_and_content: excel files were generated containing expression and differential expression with statistics and scores

organism: Drosophila melanogaster

source_name: adult fly

extract_protocol:
Total RNA was extracted from about 10, 1-week or 5-weeks old, entire or dissected (head, legs, wings and ovaries removed) adult flies, using TRIzol reagent (Invitrogen) following manufacturer’s instructions. The following genotypes dedicated for TU-tagging cell - specific transcript isolation were used: Hand>LacZ;HA-UPRT, Hand>MblRNAi;HA-UPRT, Hand>Bru3;HA-UPRT and Hand>960CTG;HA-UPRT
Library preparation was performed on about 50 ng of cardiac specific RNA from the previously described conditions, using the Ovation RNA-Seq Systems 1-16 for Model Organisms adapted to Drosophila (NuGEN, #0350-32) following manufacturer’s instructions with few modifications. First-strand synthesis was performed with the integrated DNAse treatment (HL-dsDNAse, ArcticZymes) and cDNA was fragmented using Bioruptor sonication system (Diagenode) with 30 cycles of 30 seconds ON/OFF on low power. 15 PCR cycles for library amplification were performed for 50 ng of starting RNA and a size-selection bead purification step was done using RNAClean XP beads (Agencourt AMPure, Beckman Coulter).

value: 1 week


title: Hand>960CTG-rep1


title: MEL06_T28_1c GCGTAGTA-CTCTCTAT


title: Hand>LacZ-rep2


title: Hand>MblRNAi-rep1


title: Hand>LacZ-rep1


title: MEL06_T28_1c CGATCAGT-CTCTCTAT


title: Hand>MblRNAi-rep2


title: MEL06_T28_1c TGCAGCTA-CTCTCTAT


title: Hand>Bru3-rep2


title: Hand>Bru3-rep1


title: Input-rep2


title: ATAC-seq_LV20 (P5)

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

institute: KU Leuven

description: CTATAC | Sample 4 LV20 (P5)

data_processing:
Single-end ATAC-seq raw data were analyzed using the ATAC-seq pipeline from the Kundaje lab (Version 0.3.3). Briefly, the raw reads were first trimmed using cutadapt (version 1.9.1) to remove adaptor sequence at the 3′ end. The trimmed reads were aligned to reference genome (mm10) using Bowtie2 (v2.2.6) using the ‘--local’ parameter. Single-end reads that aligned to the genome with mapping quality ≥30 were kept as usable reads (reads aligned to the mitochondrial genome were removed) using SAMtools (v1.2). PCR duplicates were removed using Picard’s MarkDuplicates (Picard v1.126).
Open chromatin regions (peak regions) were called using MACS2 (v2.1.0) using the ‘-g 1.87e9 -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits’ parameter.
The differential chromatin accessibility analysis and related plots were performed using the DiffBind package with ‘DESeq2, log2fold=1, FDR<=0.05’ parameter.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files containing open chromatin peaks normalized to the genome size

organism: Mus musculus

source_name: induced Pluripotent Stem Cells

growth_protocol: PSCs were expanded on top of male WT feeders in mouse ESC medium (S/L condition)

extract_protocol:
Next, the cell pellets were resuspended in 50 µl of ATAC-lysis buffer (10mM Tris HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, 0.1% NP40, and 0.01% Digitonin) and incubated on ice for 3 min. Wash out lysis with 1 ml of cold ATAC-lysis buffer containing 0.1% Tween-20 but No NP40 or digitonin and invert tube 3 times to mix. Nuclei were pelleted at 500 RCF for 10 min at 4°C in a fixed angle centrifuge.
Cells nuclei were resuspended in 50 µl of transposition mixture (25 ul 2x TD buffer, 2.5 ul transposase (100 nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, and 5 ul H2O) (Nextera DNA Sample Preparation Kit, Illumina, FC-121-1030). The reaction was performed  at 37°C for 30 minutes in a thermomixer with 1000 RPM mixing. The transposed DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (D4014). DNA libraries were PCR amplified using NEBNext High-Fidelity 2x PCR Master Mix (Bioke, M0541), and size selected for 200 to 800 bp using homemade Serapure beads [60]. Library concentrations were quantified with the KAPA Library Quantification Kit (KK4854), and equimolar amounts were pooled for single-end sequencing on an Illumina HiSeq 4000 instrument (Illumina) to yield ~50 million (range 34-90 million) 51bp long reads per sample.

treatment_protocol: PSCs were feeder-depleted and 50,000 viable cells were pelleted at 500 RCF at 4°C for 5 min in a fixed angle centrifuge

tag: cell type

value: iPSC

tag: gender

value: female

tag: passage

value: WT


title: ATAC-seq_LV22 (P5)

description: GACGAC | Sample 6 LV22 (P5)


title: ATAC-seq_LV22 (P13)

description: CGTACG | Sample 12 LV22 (P13)


title: ATAC-seq_LV21 (P5)

description: CTCAGA | Sample 5 LV21 (P5)


title: ATAC-seq_LV4 (P13)

description: TAATCG | Sample 7 LV4 (P13)

value: male


title: ATAC-seq_V6.5

description: ACTGAT | Sample 17 V6.5 (P11)

source_name: Embryonic Stem Cells

value: ESC


title: ATAC-seq_LV21 (P13)

description: ATGTCA | Sample 11 LV21 (P13)


title: ATAC-seq_LV20 (P13)

description: TCGGCA | Sample 10 LV20 (P13)


title: ATAC-seq_LV16 (P13)

description: TCCCGA | Sample 9 LV16 (P13)


title: ATAC-seq_LV8 (P13)

description: TCATTC | Sample 8 LV8 (P13)


title: ATAC-seq_LV16 (P5)

description: CTAGCT | Sample 3 LV16 (P5)


title: ATAC-seq_LV8 (P5)

description: CGGAAT | Sample 2 LV8 (P5)


title: ATAC-seq_LV4 (P5)

description: CCAACA | Sample 1 LV4 (P5)


title: Input-rep1


title: C671

city: León

first: Beatriz

last: Gutierrez Gil

state: León

address: Faculty of Veterinary, Campus de Vegazana

department: Dpto Animal Production

country: Spain

institute: University of León

data_processing:
FastQC program was used to assess the quality of the raw sequencing data.
We used the software STAR v2.4.0 (Dobin et al., 2013) to map the reads against the ovine genome assembly v.3.1. (Oar_v3.1).
The quantification of gene expression was performed using RSEM v.1.3.0 (Li and Dewey, 2011)
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: RSEM output containing counts per gene in each sample

organism: Ovis aries

source_name: perirenal fat

extract_protocol:
miRNeasy mini KIT from Qiagen (Valencia, CA, USA)
TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA)

tag: breed

value: Churra

tag: diet

value: suckling lamb

tag: Sex

tag: slaughter day

tag: weight (kg)


title: C668


title: C672


title: LV8 (P7)

description: GATCAG | Sample 18 LV8 (P7)

data_processing:
Reads from all datasets were aligned to mouse reference genome GRCm38/mm10 using STAR (v2.5.3a) with default parameters followed with conversion to BAM sorted by coordinate.
featureCounts function from the R Bioconductor package “Rsubread” was used to assign mapped reads to genomic features. For downstream analyses, only the genes with CPM value (count-per-milion) higher than 0.5 in at least two libraries were kept.
A read count matrix was used as an input for differential expression analysis using the edgeR quasi-likelihood pipeline in R(Chen et al. 2016). Obtained P values were corrected for multiple testing with the Benjamini–Hochberg method to control the FDR. Genes were considered significantly differentially regulated on the basis of both FDR < 0.05 and fold difference = 1.5
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with matrix for all samples with CPM values normalized by the library size

extract_protocol:
Total RNA were isolated from all biological samples using TRIzol reagent following the manufacturer’s protocol.
4 µg of total RNA was used for library preparation with the KAPA stranded mRNA Library prep kit for Illumina platform (KAPA Biosystems). Library concentrations were quantified with the Qubit dsDNA HS (High Sensitivity) Assay Kit (Invitrogen, Q32854), and equimolar amounts were pooled for single-end sequencing on an Illumina HiSeq 4000 instrument (Illumina) to yield ~20 million reads (range 13–23 million) of 36 bp or 51 bp in length per sample.

tag: differentiation time

value: undifferentiated

tag: genotype


title: LV20 (P13)

description: GTGAAACG | Sample 26 LV20 (P13)


title: LV16 (P7)

description: CTTGTA | Sample 19 LV16 (P7)


title: LV22 (P7)

description: AGTTCCGT | Sample 22 LV22 (P7)


title: LV22 (P13)

description: GTTTCGGA | Sample 28 LV22 (P13)


title: LV20 (P7)

description: GGCTAC | Sample 20 LV20 (P7)


title: LV21 (P7)

description: AGTCAACA | Sample 21 LV21 (P7)


title: LV21 (P13)

description: GTGGCCTT | Sample 27 LV21 (P13)


title: LV4 (P13)

description: ATGTCAGA | Sample 23 LV4 (P13)


title: LV16 (P13)

description: GTCCGCAC | Sample 25 LV16 (P13)


title: LV8 (P13)

description: CCGTCCCG | Sample 24 LV8 (P13)


title: C651


title: A687

value: Assaf


title: A668


title: C642


title: A663


title: A649


title: MiM-ms

city: Seoul

first: Joha

last: Park

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description: PKR fCLIP (Millipore)

data_processing:
Using cutadapt v1.10 with Python 3.5.1, sequencing reads were quality trimmed and clipped off adapter sequences. Reads shorter than 20 bases or not properly paired were discarded.
PCR duplicates were identified based on the random sequences in the 3′ adapter, which serve as unique molecular identifiers, along with a subsequence of 1:36 region of R2 (a second segment in a pair) reads. These PCR duplicates were then removed from the data.
Reads were filtered with the position of the delimiter sequence while allowing 1-base shift to exclude undesired reads.
Before mapping to the genome, R2 reads were first mapped to the common contaminants set as previously described in (Chang et al., 2014) to remove uninformative reads. After cleaning up, paired reads were mapped to the human genome (hg38) with STAR aligner (Dobin et al., 2013) with allowing multiple mapping up to 20 loci. Only uniquely mapped reads were then used in the further analyses.
To call peaks, sequencing data were binned with 500 base long non-overlapping windows, and reads within individual bin were counted. PKR or J2 data were then matched with the corresponding window in the Input samples, and fed to Piranha v1.2.1 peak caller. When running Piranha, a covariate was converted to the log scale.
Genome_build: hg38
Supplementary_files_format_and_content: (*.summ.txt) Peak calling from PKR-fCLIP HiSeq data. Similar to BED12 format. Summarized genome annotations are added to the output from Piranha v1.2.1 peak caller
Supplementary_files_format_and_content: (*.class.txt)Read counts by RNA classes.

source_name: HeLa

extract_protocol:
RNAs were purified using Acid-Phenol Chloroform and DNA was digested using DNase I (TaKaRa). To completely remove rRNA, Ribo-Zero Magnetic Kit (Epicentre) followed by NEB Next rRNA Depletion Kit (NEB) were used following the manufacturers' instructions.
RNAs were treated with CIAP and radiolabeled using PNK reaction. Labeled RNAs were then run on a 10% Urea-PAGE gel to obtain ~50-500 nt fragments and extracted using 0.3M NaCl solution. RNAs were then ligated to 3′ adaptors using T4 RNA ligase 2 truncated, KQ (TaKaRa) and run on a 10% Urea-PAGE gel to exclude free 3′ adapters. The 3′ adapter-ligated RNAs were then ligated to 5′ adapters using T4 RNA ligase 1 (TaKaRa) and then reverse transcribed using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). cDNA was then amplified using Phusion HF polymerase (NEB) and purified by running on a 6% acrylamide gel. Amplified cDNA library was then sequenced on an Illumina HiSeq 2500 platform. The sequences of the 3′ adapter, 5′ adapter, RT primer, and PCR primers used in this study are listed in Supplemental Table S2.

treatment_protocol: Cells were fixed with 0.1% paraformaldehyde (Electron Microscopy Science) at room temperature (RT) for 10 min. Immediately, cells were quenched by adding glycine and incubated at RT for additional 10 min. Crosslinked cells were lysed in the fCLIP lysis buffer (20 mM Tris-HCl, pH 7.5, 15 mM NaCl, 10 mM EDTA, 0.5% NP-40, 0.1% Triton X-100, 0.1% Sodium deoxycholate) and sonicated 3 times, 5 min each for complete lysis. The lysate was then immunoprecipitated using PKR antibody (Cell Signaling or Millipore EMD) or J2 antibody (English and Scientific Consulting Kft) for 3 hr at 4 ℃. Urea buffer (200 mM Tris-HCl pH 7.4, 100 mM NaCl, 20 mM EDTA, 2% SDS, and 7M Urea) was used to elute PKR-RNA complexes from the bead. RNA was then de-crosslinked and separated from PKR by incubating at 65 ℃ for at least 12 hr with 20 mg/ml Proteinase K (Roche).

tag: cell cycle phase

value: M phase

tag: cell line

value: HeLa

tag: fraction

value: Co-immunoprecipitated RNAs

tag: antibody

value: PKR fCLIP (Millipore)


title: J2S-ms

description: J2 fCLIP

value: S phase

value: Immunoprecipitated RNAs

value: J2 fCLIP


title: MiS-ms

description: PKR fCLIP (Millipore)


title: LV4 (P7)

description: ACTTGA | Sample 17 LV4 (P7)


title: C666


title: D7S-ms

description: PKR fCLIP (D7F7)

value: PKR fCLIP (D7F7)


title: J2M-ms

description: J2 fCLIP


title: INS-ms

description: IP input

value: Input RNAs


title: INM-ms

description: IP input


title: D7M-ms

description: PKR fCLIP (D7F7)


title: A656


title: A684


title: J2S

description:
J2 fCLIP
J2S-INS.500.summ.txt


title: J2M

description:
J2 fCLIP
J2M-INM.500.summ.txt


title: D7S

description:
PKR fCLIP
D7S-INS.500.summ.txt

value: PKR fCLIP


title: D7M

description:
PKR fCLIP
D7M-INM.500.summ.txt


title: INS

description:
IP input
D7S-INS.500.summ.txt
J2S-INS.500.summ.txt


title: INM

description:
IP input
D7M-INM.500.summ.txt
J2M-INM.500.summ.txt


title: MM1S_pLKO_CLF_2uM_24hr_1

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Sequenced reads were trimmed for adaptor sequences, and alignment was performed using tophat2
Aligned reads translated to expression counts using HTSeq
Expression normalized using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Expression counts provided as normalized expression counts

source_name: multiple myeloma cell line infected with shRNA

growth_protocol: MM1S cells were maintained in in RPMI media supplemented with 10% fetal bovine serum, 2mM glutamine, 10mM hepes  pH7.4; non-essential amino acids, 1mM sodium pyruvate and penicillin-streptomycin antibiotics; WI38 cells were maintained in DMEM media supplemented with 10% fetal bovine serum, 2mM glutamine and penicillin-streptomycin antibiotics

extract_protocol:
total RNA was isolated using the RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Exponentially growing cells were treated with 2uM or 4uM CLF, and samples collected at 0, and 24  of exposure.

value: Female

value: multiple myeloma cell line

tag: shRNA

value: pLKO

tag: treatment

value: CLF

tag: treatment time


title: MM1S_pLKO_NT-24hr_1

tag: cell type

value: untreated


title: MM1S_shAHR-2_2

tag: gender


title: MM1S_pLKO_NT_2hr_1


title: MM1S_pLKO_CLF_2uM_24hr_2


title: MM1S_pLKO_NT_2hr_2


title: MM1S_shAHR-3_2


title: MM1S_shAHR-2_1


title: MM1S_pLKO_NT_24hr_2


title: MM1S_shAHR-3_1


title: MYC binding after 8 hours of MYC activation, replicate 1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
Chip-seq data was aligned using bowtie version 0.12.9 to human genome hg38
Peak calling was done with HOMER software with IgG samples used as a control with -style factor -fdr 0.05 parameters. Comparisons between conditions were done using -fdr 0.05 -F 1 parameters
Genome_build: hg38
Supplementary_files_format_and_content: Prosessed file contains HOMER peak calling output for every non-IgG sample versus IgG control

source_name: Human colon adenocarcinoma DLD-1 cell lines (ATCC CCL-221)

growth_protocol: Human colon adenocarcinoma DLD-1 cell lines were purchased from American Type Culture Collection (ATCC CCL-221) and maintained in DMEM (Invitrogen #21063-388 029) supplemented with 10% FBS (Sigma) and 1% penicillin-streptomycin (Invitrogen).

extract_protocol:
Chromatin fragments were prepared from DLD-1: MycER cells following 8hr of MYC activation (Vehicle or 4-OHT treatment). DNA was sonicated using Covaris 200 instrument at settings of Temp 5-9, PP200, DF 10, CB 200, 720sec. 50ug DNA was used for each ChIP. The following antibodies from Santa Cruz Biotechnology were used to perform ChIP at a concentration of 5ug: ATF4 (cat# sc-200x, lot# G0115, c-20), MYC (cat# sc-764, lot#D0413, N-262), Rabbit IgG (cat# sc-2027x, lot# G2516).
Library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina #E7645S and NEBNext Multiplex Oligos for Illumina #E7335S according to manufacturer’s instructions.

treatment_protocol: DLD-1 cells and MEFs were infected with retroviruses expressing MycER. MycER was induced with 500nM of 4-hydroxytamoxifen (4-OHT, Sigma-H7904).

tag: tissue

value: MYC

tag: myc status

value: activated

tag: replicate


title: MYC binding after 8 hours of MYC activation, replicate 2

value: Human colon adenocarcinoma DLD-1 cell lines (ATCC CCL-221)


title: ATF4 binding in control condition, replicate 2

value: control


title: ATF4 binding after 8 hours of MYC activation, replicate 2


title: IgG control

description: IgG control

value: IgG


title: ATF4 binding after 8 hours of MYC activation, replicate 1


title: ATF4 binding in control condition, replicate 1


title: WI38_shAHR-4_2

source_name: normal fibroblast  cell line infected with shRNA

value: normal fibroblast  cell line


title: WI38_shAHR-4_1


title: WI38_shAHR-1_1


title: WI38_pLKO_CLF_4uM_1


title: A648

tag: breed

value: Assaf

tag: diet

value: suckling lamb

tag: Sex

value: male


title: WI38_pLKO_NT_2


title: MEL06_T10 12B_GFRA2_high

description: NexteraXT

data_processing:
BAM files were converted to merged, demultiplexed FASTQ files, cleaned using fastq-mcf (ea-utils r819), and QC checked with FastQC (0.11.4)
Reads were then mapped to the human genome (hg19) using STAR (2.4.1b) and quantified with Subread (1.4.6-p2)
GRCh37
.txt format, library size factor normalized (Deseq2)

molecule: polyA RNA

source_name: T10 melanoma cells GFRA2high sorted

extract_protocol:
Mel006 invitro cells were treated with dabrafenib and trametinib for 10-28days.
Cells were FACS sorted for GFRA2 expression (about1500cells) prior RNA extraction with Rneasy micro kit (Qiagen)

treatment_protocol: Mel006 cells were grown in RPMI 1640 supplemented with 1% PS and 10% FCS.

value: MEL006 in vitro

tag: age

value: 10d on treatment

value: BRAFmut (V600E)


title: MEL06_T10 11A_AQP1_GFRA2_low

description: NexteraXT

source_name: T10 melanoma cells GFRA2low sorted

tag: genotype


title: WI38_pLKO_CLF_4uM_2

value: Female


title: MEL06_T10 3A_GFRA2_low

description: NexteraXT


title: WI38_shAHR-1_2


title: MEL06_T28 4A_GFRA2_low

description: NexteraXT

source_name: T28 melanoma cells GFRA2low sorted

value: 28d on treatment


title: MEL06_T28 4B_GFRA2_high

description: NexteraXT

source_name: T28 melanoma cells GFRA2high sorted


title: Tres_H2.S208

description: SMARTseq2 (Picelli et a. 2014)

data_processing:
BAM files were converted to merged, demultiplexed FASTQ files, cleaned using fastq-mcf (ea-utils r819), and QC checked with FastQC (0.11.4)
Reads were then mapped to the human genome (hg19) using STAR (2.4.1b) and quantified with Subread (1.4.6-p2)
Cells with less than 100,000 reads and/or 1000 genes expressed were discarded
Furthermore, only cells with an average expression level >3 of a curated list of housekeeping genes (n=85) were kept (Tirosh et al., 2016)
low-quality cell removal: library size, genes expressed per cell, ERCCs, house-keeping gene expression and mitochondrial DNA reads (Lun et al., 2016)
GRCh37
.txt read counts

source_name: phase3 melanoma cell

extract_protocol:
FACS sorting for dsRED+ living cells, SMARTseq2 (Picelli et a. 2014)
Nextera-XT (Illumina)

treatment_protocol: BRAFi&MEKi by oral gavage

value: tumor (PDX MEL006)

value: 57d on treatment


title: MEL06_T10 3B_GFRA2_high

description: NexteraXT


title: Tres_H14.S272

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_H4.S224

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_H9.S264

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G8.S255

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G6.S239

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G7.S247

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_H6.S240

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_H11.S280

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G9.S263

description: SMARTseq2 (Picelli et a. 2014)


title: WI38_pLKO_NT_1

value: pLKO

value: untreated


title: Tres_G5.S231

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G3.S215

description: SMARTseq2 (Picelli et a. 2014)


title: MEL06_T10 11B_AQP1_GFRA2_high

description: NexteraXT


title: Tres_G1.S199

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F9.S262

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F6.S238

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F14.S270

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F1.S198

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F4.S222

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F12.S286

description: SMARTseq2 (Picelli et a. 2014)


title: A670

tag: slaughter day

tag: weight (kg)


title: Tres_F11.S278

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E7.S245

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E8.S253

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E9.S261

description: SMARTseq2 (Picelli et a. 2014)


title: Isotype control detected miRNAs, biological rep6

type: mixed

city: Düsseldorf

first: Pablo

last: Landgraf

address: Moorenstraße 5

department: Clinic of Pediatric Oncology, Hematology and Clinical Immunology

institute: Heinrich-Heine University Düsseldorf

description:
Isotype control detected miRNAs
SNB19Iso2.3

hyb_protocol: The corresponding Cy3 and Cy5 labled miRNAs were combined and hybridized overnight (16 hours, 42°C) to a miRXplore microarray (MACS molecular Miltenyi Biotec) using an a-Hyb Hybridization Station (MACS molecular Miltenyi Biotec). The microarrays were washed five times with distilled water (at room temperature) and dried with compressed, dry air.

scan_protocol: miRXplore microarrays were scanned using the Axon GenePix 4200A Microarray Scanner

data_processing:
Microarray image analysis and ratio-based normalisation of the microarray data was conducted using the software package GenePix Pro 6.1 (Molecular Devices). Data was filtered with respect to background-subtracted signal intensity, signal to noise ratio and spot diameter. Local background was subtracted from the signal to obtain the net signal intensity and the ratio of both fluorescent labels. Subsequently, the mean of the ratios of 4 corresponding spots representing the same miRNA was computed for those spots only which were unflagged (empty spots, poor spots, negative spots) and for which the fluorescent intensity in of the miRNAs derived from the samples of interest was two-fold the mean background value. The mean ratios of all probes were normalized to the median of the ratios detected for the spiked 18 synthetic RNA oligonucleotides reverse complement to miRControl 3 probes. Signal intensities of miRNAs without the corresponding miRNA in the synthetic miRNA pool were divided by the mean value of signal intensities of all detected miRNAs in the pool.
Note that positive and calibration controls disappear after the first data processing.

molecule: other

organism: synthetic construct

source_name: synthetic miRNA pool (universal reference)

label_protocol: miRNAs were 3' end labeled using a truncated and mutated RNA ligase Rnl2(1-249)K227Q

extract_protocol: TRIzol extraction of Ago- / isotype control-associated and total RNA was performed according to the manufacturer's instructions.

tag: sample type

value: 1 fmol of each of 771 synthetic miRNAs were pooled and labeled

source_name: SNB19 cell line, 4'-thiouridine and UV treated

value: human astrocytoma (derivative of U-251 MG)

tag: cell line

value: glioma-derived cell line

value: cells were harvested after 48 - 72 h when they reached 80% confluence

tag: monoclonal antibody

value: antibody isotype control

tag: monoclonal antibody supplier

value: collaborator Gunter Meister, Department of Biochemistry, Laboratory of RNA Biology, Universit t Regensburg, Universit tsstrasse 31, 93053 Regensburg, Germany


title: Identified miRNAs of total RNA, biological rep3

description:
Gene expression data from miRNAs of total RNA of SNB19 cells
SNB19totalRNA3


title: Identified miRNAs of total RNA, biological rep1

description:
Gene expression data from miRNAs of total RNA of SNB19 cells
SNB19totalRNA1


title: Identified miRNAs of total RNA, biological rep2

description:
Gene expression data from miRNAs of total RNA of SNB19 cells
SNB19totalRNA2


title: Isotype control detected miRNAs, biological rep5

description:
Isotype control detected miRNAs
SNB19Iso2.2


title: Isotype control detected miRNAs, biological rep7

description:
Isotype control detected miRNAs
SNB19Iso3


title: Isotype control detected miRNAs, biological rep1

description:
Isotype control detected miRNAs
SNB19Iso1.1


title: Isotype control detected miRNAs, biological rep3

description:
Isotype control detected miRNAs
SNB19Iso1.3


title: Isotype control detected miRNAs, biological rep2

description:
Isotype control detected miRNAs
SNB19Iso1.2


title: Isotype control detected miRNAs, biological rep4

description:
Isotype control detected miRNAs
SNB19Iso2.1


title: Tres_F8.S254

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F7.S246

description: SMARTseq2 (Picelli et a. 2014)


title: Ago3-associated miRNAs, biological rep3

description:
Identification of Ago3-associated miRNAs
SNB19Ago3.3


title: Ago2-associated miRNAs, biological rep2

description:
Identification of Ago2-associated miRNAs
SNB19Ago2.2


title: Ago1-associated miRNAs, biological rep3

description:
Identification of Ago1-associated miRNAs
SNB19Ago1.3


title: Ago2-associated miRNAs, biological rep1

description:
Identification of Ago2-associated miRNAs
SNB19Ago2.1


title: Ago1-associated miRNAs, biological rep2

description:
Identification of Ago1-associated miRNAs
SNB19Ago1.2


title: Ago3-associated miRNAs, biological rep1

description:
Identification of Ago3-associated miRNAs
SNB19Ago3.1


title: Tres_E5.S229

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E6.S237

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E4.S221

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E3.S213

description: SMARTseq2 (Picelli et a. 2014)


title: Ago3-associated miRNAs, biological rep2

description:
Identification of Ago3-associated miRNAs
SNB19Ago3.2


title: Ago2-associated miRNAs, biological rep3

description:
Identification of Ago2-associated miRNAs
SNB19Ago2.3


title: Tres_E1.S197

description: SMARTseq2 (Picelli et a. 2014)


title: Ago1-associated miRNAs, biological rep1

description:
Identification of Ago1-associated miRNAs
SNB19Ago1.1


title: Tres_D4.S220

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D6.S236

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D7.S244

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D3.S212

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D5.S228

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D8.S252

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C6.S235

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C5.S227

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D12.S284

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D1.S196

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C8.S251

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C7.S243

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D11.S276

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C1.S195

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E12.S285

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C14.S267

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C9.S259

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C4.S219

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D14.S268

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C3.S211

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B4.S218

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B6.S234

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B7.S242

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B14.S266

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B12.S282

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B1.S194

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B3.S210

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B11.S274

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E11.S277

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_A8.S249

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_A6.S233

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_A4.S217

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_A14.S265

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_A7.S241

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_H9.S381

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_H8.S373

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_H3.S333

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_H5.S349

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_H2.S325

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_H12.S97

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_H10.S113

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_H11.S105

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G1.S316

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_H1.S317

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G4.S340

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G7.S364

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G2.S324

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G12.S98

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G3.S332

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G11.S106

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G10.S114

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F7.S363

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F8.S371

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F9.S379

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_A11.S273

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G6.S356

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G8.S372

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_G9.S380

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F3.S331

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E4.S338

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F2.S323

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F1.S315

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E10.S116

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F11.S107

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E6.S354

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E11.S108

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F6.S355

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E8.S370

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E2.S322

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E7.S362

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E12.S100

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D6.S353

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F10.S115

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E3.S330

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E9.S378

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_F5.S347

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E5.S346

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D8.S369

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D3.S329

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D5.S345

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_E1.S314

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D7.S361

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D12.S101

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D1.S313

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D2.S321

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D10.S117

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_D11.S109

description: SMARTseq2 (Picelli et a. 2014)


title: TTR12

city: Shanghai

first: Yunbin

last: Zhang

address: No. 320, Yueyang Road, Xuhui District

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

description: Human retinal endothelial cells (hRECs) from passage 4 were diluted to 8×104/mL and incubated in 6-well plates with low glucose (LG) media until confluent. After washing with PBS, the cells were further cultured for 48 h at 37 °C in low glucose (LG), high glucose (HG), or high glucose with 4 uM TTR (HG+TTR) media.

data_processing:
Raw reads were trimmed using Skewer, then mapped to GRCh38.90 whole genome using STAR verison 2.5.2b with parameters --twopassMode Basic --outSAMstrandField intronMotif --alignSJstitchMismatchNmax 5 -1 5 5
Transcripts were assembled by StringTie, FPKM and raw read counts were calculated using ballgown
DESeq2 was used for all differential expression analysis from the raw read counts
Genome_build: GRCh38.90
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Human retinal endothelial cells (hRECs)

extract_protocol:
Cells were collected and total RNAs were extracted from hRECs, using TRIzol reagent (Takara, Dalian, China), according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human retinal endothelial cells (hRECs)

tag: treatment

value: high glucose+4 uM TTR


title: Tres_C9.S376

description: SMARTseq2 (Picelli et a. 2014)


title: TTR2

tag: cell type


title: Tres_C8.S368

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C7.S360

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C6.S352

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C12.S102

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C4.S336

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C10.S384

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C1.S312

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B7.S359

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C3.S328

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_C2.S320

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B6.S351

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B3.S327

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B5.S343

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B11.S111

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B1.S311

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B2.S319

description: SMARTseq2 (Picelli et a. 2014)


title: ditang2

value: low glucose


title: Tres_B10.S383

description: SMARTseq2 (Picelli et a. 2014)


title: gaotang12

value: high glucose


title: Tres_A9.S374

description: SMARTseq2 (Picelli et a. 2014)

value: BRAFmut (V600E)


title: gaotang2


title: Tres_B4.S335

description: SMARTseq2 (Picelli et a. 2014)


title: gaotang1


title: ditang1


title: TTR1


title: Tres_C11.S110

description: SMARTseq2 (Picelli et a. 2014)


title: ditang12


title: Tres_A8.S366

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_A7.S358

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_A5.S342

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_A6.S350

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_A12.S104

description: SMARTseq2 (Picelli et a. 2014)


title: lib2_AR_T28_2_G5.S268

description: SMARTseq2 (Picelli et a. 2014)

source_name: phase2 melanoma cell


title: Tres_A1.S310

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_A4.S334

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_A11.S112

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_A10.S382

description: SMARTseq2 (Picelli et a. 2014)


title: Tres_B12.S103

description: SMARTseq2 (Picelli et a. 2014)


title: lib2_AR_T28_2_D5.S232

description: SMARTseq2 (Picelli et a. 2014)


title: lib2_AR_lib2_AR_T28_228_2_G6.S269

description: SMARTseq2 (Picelli et a. 2014)


title: lib2_AR_lib2_AR_T28_228_2_G11.S274

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M of dbf2-2 mutant, rep 3

city: Barcelona

first: Alsu

last: Missarova

address: Dr. Aiguader, 88

department: CEXS

institute: UPF

data_processing:
All .fastq.gz files were trimmed from adapters using Trimmomatic. Options: MINLEN = 25; Adapter fasta files = TruSeq2-PE.fa:2:30:10; -phred33; PE;
Trimmed .fastq.gz files were mapped using BWA-MEM algorithm
Coverage was calculated over windows of 200bp, for all gDNA
Copy Number (:= CN) for each sample was calculated as coverage divided to the mode of all coverage data, each sample/chromosome separetely
To calculate final CN: we applied a local regression to CN using a weighted linear least squares and a first degree polynomial model (with a 5kb span)
Genome_build: R64
processed data files: $name$_CN.tab; 5 columns: chr; start-point; end-point; coverage; final CN
processed data files: stat__2017_10_06.tab: for each 200-bp window: median of CN-ratio (for both, metaphase arrest -- denoted with _M and late anaphase arrest -- denoted with _T) and under-replication across repeatable replicates (for both, metaphase arrest -- denoted with _M and late anaphase arrest -- denoted with _T)

organism: Saccharomyces cerevisiae

source_name: arrest_M of dbf2-2 mutant

extract_protocol:
phenol-chloroform-isoamyl DNA extraction
TruSeq DNA PCR-free

tag: cell cycle stage

value: M (late anaphase/telophase)

value: dbf2-2 mutant


title: arrest_M of dbf2-2 mutant, rep 5


title: lib2_AR_lib2_AR_T28_228_2_G7.S270

description: SMARTseq2 (Picelli et a. 2014)

tag: tissue

value: tumor (PDX MEL006)

value: 28d on treatment


title: lib2_AR_T28_2_C5.S220

description: SMARTseq2 (Picelli et a. 2014)


title: lib2_AR_lib2_AR_T28_228_2_F6.S257

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_G1 of dbf2-2 mutant, rep 3

source_name: arrest_G1 of dbf2-2 mutant


title: arrest_G1 of dbf2-2 mutant, rep 5


title: arrest_M of dbf2-2 mutant, rep 6


title: lib2_AR_lib2_AR_T28_228_2_G10.S273

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M of dbf2-2 mutant, rep 2


title: arrest_M of dbf2-2 mutant, rep 1

description: not repeatable, excluded from the further analyses


title: arrest_G1 of dbf2-2 mutant, rep 4


title: lib2_AR_lib2_AR_T28_228_2_F4.S255

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_G1 of dbf2-2 mutant, rep 2


title: lib2_AR_lib2_AR_T28_228_2_F3.S254

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_G1 of dbf2-2 mutant, rep 6


title: lib2_AR_lib2_AR_T28_228_2_F12.S263

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_G1 of dbf2-2 mutant, rep 1


title: arrest_M of cdc20 mutant, rep 6

source_name: arrest_M of cdc20 mutant

value: M (metaphase)

value: cdc20 mutant


title: arrest_M of dbf2-2 mutant, rep 4


title: lib2_AR_lib2_AR_T28_228_2_F11.S262

description: SMARTseq2 (Picelli et a. 2014)


title: lib2_AR_lib2_AR_T28_228_2_E8.S247

description: SMARTseq2 (Picelli et a. 2014)


title: lib2_AR_lib2_AR_T28_228_2_E7.S246

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M of cdc20 mutant, rep 4


title: arrest_M of cdc20 mutant, rep 3


title: lib2_AR_lib2_AR_T28_228_2_E3.S242

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M of cdc20 mutant, rep 2


title: lib2_AR_lib2_AR_T28_228_2_E2.S241

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M of cdc20 mutant, rep 1


title: lib2_AR_lib2_AR_T28_228_2_D6.S233

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_G1 of cdc20 mutant, rep 6

source_name: arrest_G1 of cdc20 mutant


title: lib2_AR_lib2_AR_T28_228_2_D9.S236

description: SMARTseq2 (Picelli et a. 2014)


title: lib2_AR_lib2_AR_T28_228_2_E11.S250

description: SMARTseq2 (Picelli et a. 2014)


title: lib2_AR_lib2_AR_T28_228_2_D3.S230

description: SMARTseq2 (Picelli et a. 2014)


title: lib2_AR_lib2_AR_T28_228_2_D10.S237

description: SMARTseq2 (Picelli et a. 2014)


title: lib2_AR_lib2_AR_T28_228_2_C9.S224

description: SMARTseq2 (Picelli et a. 2014)


title: lib2_AR_lib2_AR_T28_228_2_C8.S223

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M-CDK inhibited rep6

data_processing:
All .fastq.gz files were trimmed from adapters using Trimmomatic. Options: MINLEN = 25; Adapter fasta files = TruSeq2-PE.fa:2:30:10; -phred33; PE;
Trimmed .fastq.gz files were mapped using BWA-MEM algorithm
Coverage was calculated over windows of 200bp, for all gDNA
Copy Number (:= CN) for each sample was calculated as coverage divided to the mode of all coverage data, each sample/chromosome separetely
To calculate final CN: we applied a local regression to CN using a weighted linear least squares and a first degree polynomial model (with a 5kb span)
Genome_build: R64
processed data files: $name$_CN.tab; 5 columns: chr; start-point; end-point; coverage; final CN
processed data files: stat__2017_09_15.tab: for each 200-bp window: median of CN-ratio (for both, metaphase arrest solely -- denoted with _M and metaphase arrest + CDK inhibition -- denoted with _S) and under-replication across repeatable replicates (for both, metaphase arrest solely -- denoted with _M and metaphase arrest + CDK inhibition -- denoted with _S)

source_name: arrest_M-CDK inhibited

value: M & CDK inhibited

tag: genotype/variation

value: strain with methionine-sensitive promoter, placed in front of CDC20


title: arrest_G1 of cdc20 mutant, rep 5


title: arrest_G1 of cdc20 mutant, rep 3


title: lib2_AR_lib2_AR_T28_228_2_C4.S219

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_G1 of cdc20 mutant, rep 1


title: lib2_AR_lib2_AR_T28_228_2_C6.S221

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M-CDK inhibited rep4


title: arrest_M of cdc20 mutant, rep 5


title: arrest_M-CDK inhibited rep3


title: lib2_AR_lib2_AR_T28_228_2_C1.S216

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M-CDK inhibited rep2


title: lib2_AR_lib2_AR_T28_228_2_C2.S217

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_H5.S376

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_H2.S373

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_G1 of cdc20 mutant, rep 4


title: arrest_M-CDK inhibited rep1


title: lib1_AR_T28_1_G9.S368

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M rep6

value: M


title: arrest_M rep5


title: arrest_G1 of cdc20 mutant, rep 2


title: lib1_AR_T28_1_G8.S367

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M rep4


title: arrest_M-CDK inhibited rep5


title: lib1_AR_T28_1_G7.S366

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_G6.S365

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M rep3


title: arrest_G1 rep3


title: lib1_AR_T28_1_G2.S361

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_G1 rep2


title: lib1_AR_T28_1_G3.S362

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M rep2


title: lib1_AR_T28_1_G1.S360

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_G1 rep1


title: lib1_AR_T28_1_G4.S363

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M rep 5

data_processing:
All .fastq.gz files were trimmed from adapters using Trimmomatic. Options: MINLEN = 25; Adapter fasta files = TruSeq2-PE.fa:2:30:10; -phred33; PE;
Trimmed .fastq.gz files were mapped using BWA-MEM algorithm
Coverage was calculated over windows of 200bp, for all gDNA
Copy Number (:= CN) for each sample was calculated as coverage divided to the mode of all coverage data, each sample/chromosome separetely
To calculate final CN: we applied a local regression to CN using a weighted linear least squares and a first degree polynomial model (with a 5kb span)
Genome_build: R64
processed data files: $name$_CN.tab; 5 columns: chr; start-point; end-point; coverage; final CN
processed data files: stat__2017_03_23.tab: for each 200-bp window: median of CN-ratio and under-replication across repeatable replicates


title: lib1_AR_T28_1_G12.S371

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M rep 6


title: arrest_M rep 3


title: arrest_M rep 4


title: lib1_AR_T28_1_G5.S364

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_G11.S370

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_G10.S369

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M rep 2


title: arrest_M rep 1


title: lib1_AR_T28_1_F7.S354

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_G1 rep 3


title: lib1_AR_T28_1_F6.S353

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_F9.S356

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_M rep1


title: arrest_G1 rep 2


title: lib1_AR_T28_1_F5.S352

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_F8.S355

description: SMARTseq2 (Picelli et a. 2014)


title: arrest_G1 rep 1


title: lib1_AR_T28_1_F4.S351

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_F3.S350

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_F12.S359

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_F1.S348

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_F11.S358

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_F10.S357

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_E9.S344

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_E8.S343

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_E5.S340

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_E4.S339

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_E2.S337

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_E1.S336

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_E11.S346

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_F2.S349

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_E10.S345

description: SMARTseq2 (Picelli et a. 2014)


title: e1 c587>tkvRNAi

city: Taipei

first: Hweijan

last: Hsu

address: no 128, Sec 2,  Academia Rd. Nankang

department: Institute of Cellular Biology

country: Taiwan

institute: Academia Research

data_processing:
Illumina bcl2fastq v2.17 software was used for basecalling.
Sequencing reads were trimmed for adaptor and low-quality sequences using Trimmomatic v0.32, then mapped to the Drosophila reference genome sequence (BDGP6) using Tophat v2.0.12 with default parameters.
Differential gene and transcript expression analysis was performed using Cufflinks package v2.2.1 to obtain the Reads Per Kilobase of exon per Megabase (RPKM) of each gene or transcript for each sample and their log2 ratios for the paired samples.  Differential expressed genes or transcripts were selected using the criteria that the RPKM fold change >=2 and the p-value lower than 0.05.
Genome_build: BDGP6
Supplementary_files_format_and_content: Excel xlsx files include RPKM values, ratios, log2 ratios and p-values for each sample and sample pair

source_name: ovary

growth_protocol: Flies with the genotype: UAS-tkvRNAi/+ (control) and c587-GAL4>UAS-tkvRNAi (experiment) were grew at 29 degree.

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA), and followed by RNeasy Mini Kit (Qiagen, Germany). RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 nano labchip kit (Agilent Technologies, USA).
Library construction for all samples was accomplished with Agilent's SureSelect Strand Specific RNA library Preparation Kit for 75SE (Single-End) sequencing on Illumina platform.

value: ovary

value: one-day-old


title: e2 c587>tkvRNAi


title: c2 UAS-tkvRNAi/+

value: UAS-tkvRNAi/+


title: lib1_AR_T28_1_D9.S332

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_D8.S331

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_D7.S330

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_E7.S342

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_D6.S329

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_D5.S328

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_D4.S327

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_D1.S324

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_D12.S335

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_C9.S320

description: SMARTseq2 (Picelli et a. 2014)


title: Ago1-associated mRNAs, biological rep1

description:
Identification of Ago1-associated mRNAs
SNB19Ago1.1

hyb_protocol: Following fragmentation, aRNA was hybridized on Affymetrix Human Genome U133 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (performed by the core facility BMFZ Düsseldorf).

scan_protocol: GeneChips were scanned using the GCS 3000 from Affymetrix (performed by the core facility BMFZ, Düsseldorf).

data_processing: The data were analyzed with RMAExpress v.1.0.4 for Windows, using quantile normalization and the median polish signal estimation algorithm.

label: biotin

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from (GeneChip 3' IVT Express Kit Manual, 2008-2009, Affymetrix).

value: human astrocytoma (derivative of U-251 MG)

value: glioma-derived cell line

value: cells were harvested after 48 - 72 h when they reached 80% confluence

value: collaborator Gunter Meister, Department of Biochemistry, Laboratory of RNA Biology, Universit t Regensburg, Universit tsstrasse 31, 93053 Regensburg, Germany


title: c1 UAS-tkvRNAi/+


title: Isotype control detected mRNAs, biological rep2

description:
Isotype control detected mRNAs (unspecific bound mRNAs of isotype control)
SNB19Iso2

value: antibody isotype control


title: lib1_AR_T28_1_D10.S333

description: SMARTseq2 (Picelli et a. 2014)

value: BRAFmut (V600E)


title: Ago3-associated mRNAs, biological rep2

description:
Identification of Ago3-associated mRNAs
SNB19Ago3.2


title: Isotype control detected mRNAs, biological rep1

description:
Isotype control detected mRNAs (unspecific bound mRNAs of isotype control)
SNB19Iso1


title: Ago3-associated mRNAs, biological rep3

description:
Identification of Ago3-associated mRNAs
SNB19Ago3.3


title: lib1_AR_T28_1_B2.S301

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_B1.S300

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_C5.S316

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_B7.S306

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_C6.S317

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_C11.S322

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_C12.S323

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_C3.S314

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_B8.S307

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_B5.S304

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_C7.S318

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_C4.S315

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_B9.S308

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_B3.S302

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_C2.S313

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_C1.S312

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_B10.S309

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_B11.S310

description: SMARTseq2 (Picelli et a. 2014)


title: identified mRNAs of total RNA

description:
Gene expression data from mRNAs of total RNA of SNB19 cells
SNB19totalRNA


title: Ago1-associated mRNAs, biological rep2

description:
Identification of Ago1-associated mRNAs
SNB19Ago1.2


title: lib1_AR_T28_1_B4.S303

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_B12.S311

description: SMARTseq2 (Picelli et a. 2014)


title: Ago3-associated mRNAs, biological rep1

description:
Identification of Ago3-associated mRNAs
SNB19Ago3.1


title: Ago2-associated mRNAs, biological rep2

description:
Identification of Ago2-associated mRNAs
SNB19Ago2.2


title: Ago1-associated mRNAs, biological rep3

description:
Identification of Ago1-associated mRNAs
SNB19Ago1.3


title: lib1_AR_T28_1_A8.S295

description: SMARTseq2 (Picelli et a. 2014)


title: Isotype control detected mRNAs, biological rep3

description:
Isotype control detected mRNAs (unspecific bound mRNAs of isotype control)
SNB19Iso3


title: lib1_AR_T28_1_A4.S291

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_A7.S294

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_A11.S298

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_A10.S297

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_A2.S289

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_A1.S288

description: SMARTseq2 (Picelli et a. 2014)


title: lib1_AR_T28_1_A12.S299

description: SMARTseq2 (Picelli et a. 2014)


title: T28_H8.S160

description: SMARTseq2 (Picelli et a. 2014)


title: T28_H11.S184

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F8.S158

description: SMARTseq2 (Picelli et a. 2014)


title: T28_G14.S175

description: SMARTseq2 (Picelli et a. 2014)


title: T28_G3.S119

description: SMARTseq2 (Picelli et a. 2014)


title: T28_G2.S111

description: SMARTseq2 (Picelli et a. 2014)


title: T28_H5.S136

description: SMARTseq2 (Picelli et a. 2014)


title: Ago2-associated mRNAs, biological rep3

description:
Identification of Ago2-associated mRNAs
SNB19Ago2.3


title: T28_G5.S135

description: SMARTseq2 (Picelli et a. 2014)


title: T28_G9.S167

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F5.S134

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F7.S150

description: SMARTseq2 (Picelli et a. 2014)


title: T28_G12.S191

description: SMARTseq2 (Picelli et a. 2014)


title: T28_G7.S151

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F6.S142

description: SMARTseq2 (Picelli et a. 2014)


title: T28_H6.S144

description: SMARTseq2 (Picelli et a. 2014)


title: T28_H12.S192

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F4.S126

description: SMARTseq2 (Picelli et a. 2014)


title: Ago2-associated mRNAs, biological rep1

description:
Identification of Ago2-associated mRNAs
SNB19Ago2.1


title: T28_F3.S118

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F14.S174

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F12.S190

description: SMARTseq2 (Picelli et a. 2014)


title: T28_E14.S173

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F11.S182

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D4.S124

description: SMARTseq2 (Picelli et a. 2014)


title: T28_E12.S189

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D6.S140

description: SMARTseq2 (Picelli et a. 2014)


title: T28_E8.S157

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D14.S172

description: SMARTseq2 (Picelli et a. 2014)


title: T28_C12.S187

description: SMARTseq2 (Picelli et a. 2014)


title: T28_C6.S139

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D7.S148

description: SMARTseq2 (Picelli et a. 2014)


title: T28_B5.S130

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D5.S132

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D3.S116

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D11.S180

description: SMARTseq2 (Picelli et a. 2014)


title: T28_C2.S107

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A9.S161

description: SMARTseq2 (Picelli et a. 2014)


title: T28_B12.S186

description: SMARTseq2 (Picelli et a. 2014)


title: T28_C8.S155

description: SMARTseq2 (Picelli et a. 2014)


title: T28_C7.S147

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A14.S169

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A7.S145

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A3.S113

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A2.S105

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A8.S153

description: SMARTseq2 (Picelli et a. 2014)


title: T28_H5.S253

description: SMARTseq2 (Picelli et a. 2014)


title: T28_H3.S237

description: SMARTseq2 (Picelli et a. 2014)


title: T28_H1.S221

description: SMARTseq2 (Picelli et a. 2014)


title: T28_G5.S252

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A11.S177

description: SMARTseq2 (Picelli et a. 2014)


title: T28_G3.S236

description: SMARTseq2 (Picelli et a. 2014)


title: T28_G2.S228

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F8.S275

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F4.S243

description: SMARTseq2 (Picelli et a. 2014)


title: T28_E7.S266

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F12.S307

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F2.S227

description: SMARTseq2 (Picelli et a. 2014)


title: T28_E5.S250

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F10.S291

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F11.S299

description: SMARTseq2 (Picelli et a. 2014)


title: T28_E6.S258

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F1.S219

description: SMARTseq2 (Picelli et a. 2014)


title: T28_E4.S242

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D1.S217

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D4.S241

description: SMARTseq2 (Picelli et a. 2014)


title: T28_E12.S306

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D7.S265

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D8.S273

description: SMARTseq2 (Picelli et a. 2014)


title: T28_G4.S244

description: SMARTseq2 (Picelli et a. 2014)


title: T28_E2.S226

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D12.S305

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D3.S233

description: SMARTseq2 (Picelli et a. 2014)


title: T28_G11.S300

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D6.S257

description: SMARTseq2 (Picelli et a. 2014)


title: T28_G10.S292

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F5.S251

description: SMARTseq2 (Picelli et a. 2014)


title: T28_D11.S297

description: SMARTseq2 (Picelli et a. 2014)


title: T28_C8.S272

description: SMARTseq2 (Picelli et a. 2014)


title: T28_C9.S280

description: SMARTseq2 (Picelli et a. 2014)


title: T28_F3.S235

description: SMARTseq2 (Picelli et a. 2014)


title: T28_E8.S274

description: SMARTseq2 (Picelli et a. 2014)


title: T28_E3.S234

description: SMARTseq2 (Picelli et a. 2014)


title: T28_C6.S256

description: SMARTseq2 (Picelli et a. 2014)


title: T28_C5.S248

description: SMARTseq2 (Picelli et a. 2014)


title: T28_B4.S239

description: SMARTseq2 (Picelli et a. 2014)


title: T28_C1.S216

description: SMARTseq2 (Picelli et a. 2014)


title: T28_B5.S247

description: SMARTseq2 (Picelli et a. 2014)


title: T28_B6.S255

description: SMARTseq2 (Picelli et a. 2014)


title: T28_B3.S231

description: SMARTseq2 (Picelli et a. 2014)


title: T28_B11.S295

description: SMARTseq2 (Picelli et a. 2014)


title: T28_B12.S303

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A8.S270

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A7.S262

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A6.S254

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A5.S246

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A12.S302

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A1.S214

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A11.S294

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G9.S71

description: SMARTseq2 (Picelli et a. 2014)

source_name: phase1 melanoma cell

value: 4d on treatment


title: T4_H11.S88

description: SMARTseq2 (Picelli et a. 2014)

value: tumor (PDX MEL006)


title: T4_H1.S8

description: SMARTseq2 (Picelli et a. 2014)


title: T4_H5.S40

description: SMARTseq2 (Picelli et a. 2014)


title: T4_H4.S32

description: SMARTseq2 (Picelli et a. 2014)


title: T28_C2.S224

description: SMARTseq2 (Picelli et a. 2014)

value: 28d on treatment


title: T4_H2.S16

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G8.S63

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G7.S55

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G2.S15

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G3.S23

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G14.S79

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G12.S95

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F9.S70

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G11.S87

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F8.S62

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F7.S54

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F5.S38

description: SMARTseq2 (Picelli et a. 2014)


title: T28_A10.S286

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F1.S6

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F11.S86

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F3.S22

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E8.S61

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E9.S69

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F14.S78

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E6.S45

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E7.S53

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G6.S47

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E2.S13

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E4.S29

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E14.S77

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E5.S37

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E3.S21

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D7.S52

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D9.S68

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E1.S5

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F6.S46

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D3.S20

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D14.S76

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D4.S28

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D2.S12

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D12.S92

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D1.S4

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C8.S59

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C7.S51

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D11.S84

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C9.S67

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C6.S43

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F12.S94

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C5.S35

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C14.S75

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B7.S50

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C3.S19

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C2.S11

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C1.S3

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B6.S42

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B4.S26

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C11.S83

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B9.S66

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B12.S90

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B3.S18

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B11.S82

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B14.S74

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C12.S91

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B1.S2

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B2.S10

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A7.S49

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A1.S1

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A14.S73

description: SMARTseq2 (Picelli et a. 2014)


title: T4_H8.S181

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A6.S41

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A2.S9

description: SMARTseq2 (Picelli et a. 2014)


title: T4_H5.S157

description: SMARTseq2 (Picelli et a. 2014)


title: T4_H4.S149

description: SMARTseq2 (Picelli et a. 2014)


title: T4_H3.S141

description: SMARTseq2 (Picelli et a. 2014)


title: T4_H11.S205

description: SMARTseq2 (Picelli et a. 2014)


title: T4_H1.S125

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G9.S188

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G8.S180

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G6.S164

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G4.S148

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G5.S156

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G3.S140

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G11.S204

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G10.S196

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F9.S187

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G12.S212

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A11.S81

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F7.S171

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G1.S124

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F5.S155

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F8.S179

description: SMARTseq2 (Picelli et a. 2014)


title: T4_H2.S133

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F4.S147

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F12.S211

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F11.S203

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F10.S195

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F3.S139

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E8.S178

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E7.S170

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E9.S186

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E5.S154

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E6.S162

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E4.S146

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E3.S138

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E1.S122

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E2.S130

description: SMARTseq2 (Picelli et a. 2014)


title: T4_G2.S132

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E12.S210

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F6.S163

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D7.S169

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E11.S202

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D6.S161

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D9.S185

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D8.S177

description: SMARTseq2 (Picelli et a. 2014)


title: T4_E10.S194

description: SMARTseq2 (Picelli et a. 2014)


title: T4_F2.S131

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D3.S137

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D10.S193

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D5.S153

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D12.S209

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D2.S129

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D4.S145

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C9.S184

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C7.S168

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C6.S160

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C8.S176

description: SMARTseq2 (Picelli et a. 2014)


title: T4_D11.S201

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C2.S128

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C1.S120

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C12.S208

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C11.S200

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C3.S136

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C10.S192

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B9.S183

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B6.S159

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B8.S175

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B5.S151

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B1.S119

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B12.S207

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B4.S143

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B3.S135

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A8.S174

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B10.S191

description: SMARTseq2 (Picelli et a. 2014)


title: T4_B11.S199

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A9.S182

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C4.S144

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A7.S166

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A6.S158

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A11.S198

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A3.S134

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A12.S206

description: SMARTseq2 (Picelli et a. 2014)


title: T4_C5.S152

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H8.S352

description: SMARTseq2 (Picelli et a. 2014)

source_name: T0 melanoma cell

value: before treatment


title: T4_A10.S190

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A1.S118

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A5.S150

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H1.S296

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H10.S368

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G9.S359

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G6.S335

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G8.S351

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G7.S343

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G1.S295

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G2.S303

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G3.S311

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G11.S375

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G10.S367

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F7.S342

description: SMARTseq2 (Picelli et a. 2014)


title: T4_A2.S126

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F8.S350

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F9.S358

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H4.S320

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F6.S334

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F4.S318

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F3.S310

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F11.S374

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F5.S326

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H11.S376

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F1.S294

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G5.S327

description: SMARTseq2 (Picelli et a. 2014)


title: T0_G4.S319

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E9.S357

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F10.S366

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E3.S309

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E8.S349

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E6.S333

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E1.S293

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E7.S341

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E5.S325

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E10.S365

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E11.S373

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D7.S340

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D6.S332

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D4.S316

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D2.S300

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D1.S292

description: SMARTseq2 (Picelli et a. 2014)


title: T0_F2.S302

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D11.S372

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D10.S364

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C9.S355

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E4.S317

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C8.S347

description: SMARTseq2 (Picelli et a. 2014)


title: T0_E2.S301

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C7.S339

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C4.S315

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C6.S331

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C3.S307

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C11.S371

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C10.S363

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B9.S354

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C2.S299

description: SMARTseq2 (Picelli et a. 2014)


title: T0_C1.S291

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B8.S346

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B6.S330

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D8.S348

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B7.S338

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B5.S322

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D3.S308

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B4.S314

description: SMARTseq2 (Picelli et a. 2014)


title: T0_D5.S324

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B3.S306

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B1.S290

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B2.S298

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B12.S378

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B11.S370

description: SMARTseq2 (Picelli et a. 2014)


title: T0_B10.S362

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A9.S353

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A8.S345

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A6.S329

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A5.S321

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A4.S313

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A3.S305

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A2.S297

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H9.S72

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A1.S289

description: SMARTseq2 (Picelli et a. 2014)


title: T0_A10.S361

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H6.S48

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H4.S32

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H8.S64

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H7.S56

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H3.S24

description: SMARTseq2 (Picelli et a. 2014)


title: T0_H2.S16

description: SMARTseq2 (Picelli et a. 2014)