title: 254706910132_b3 - 3A_WT_untreated_1 vs 4A_WT_Rotenone7d_1

hyb_protocol: 4A_WT_Rotenone7d_1 Cy5 / 3A_WT_untreated_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Myc.Tgfa_15

status: Public on Jan 01 2019

type: RNA

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

country: USA

institute: Baylor Colleage of Medicine

description: Twenty micrograms of total RNA from tissues were used to derive fluorescently (Cy5 or Cy3) labeled complementary DNA. A reference complementary DNA was generated using total RNA from 19 normal livers. At least two hybridizations were performed for each tissue sample using a dye-swap strategy to eliminate labeling bias of the fluorescent intensity measurement.

hyb_protocol: At least two hybridizations were carried out for each tissue using dye-swap strategy to eliminate dye labeling bias.

scan_protocol: Scanned with Axon GenePix 4000B, images and spot values acquired with GenePix Pro 5.1.0.19

data_processing: We transformed and normalized mouse gene expression and  averaged expression ratios of each gene from replicated experiments , selected genes with <30% missing expression data across the tissues in each data set and an expression ratio that differed from reference by a factor of at least 2 in at least 10% of tissues in each data set for further analysis

molecule: total RNA

organism: Mus musculus

source_name: HCC tumor

label_protocol: To obtain gene expression profile data from four transgenic HCC mouse models, 20 μg of total RNAs from tissues were used to drive fluorescently (Cy-5 or Cy-3) labeled cDNA.

extract_protocol: Total RNAs were isolated from frozen liver tissue using CsCl density gradient centrifugation methods. Total RNA from the livers of 10 wild type mice were pooled and used as reference in entire microarray experiments.

tag: genotype/variation

value: transgenic mice expressing Myc/transforming growth factor alpha (Tgfa)

tag: tissue

value: liver


title: 254706910133_b3 - 3C_WT_untreated_3 vs 4C_WT_Rotenone7d_3

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: How does inhibition of CI enhance organogenesis?

hyb_protocol: 4C_WT_Rotenone7d_3 Cy5 / 3C_WT_untreated_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%

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

organism: Arabidopsis thaliana

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

growth_protocol: callus - Média: Arabidopsis liquid medium hygrometry: 70% Temperature: 21°C Light: 10h day / 12h night

treatment_protocol: Name:Rotenone on callus - time course study - inhibition of mitochodrial etc,rotenone:. Inhibition of the the comlex I of the mitochodrial electron transport chain with rotenone

tag: ecotype

value: Columbia

tag: harvest date

treatment_protocol: no treatment


title: 254706910132_b1 - 1C_WT_untreated_3 vs 2C_WT_Rotenone12h_3

hyb_protocol: 2C_WT_Rotenone12h_3 Cy5 / 1C_WT_untreated_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910133_b1 - 3B_WT_untreated_2 vs 4B_WT_Rotenone7d_2

hyb_protocol: 4B_WT_Rotenone7d_2 Cy5 / 3B_WT_untreated_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910133_b2 - 4B_WT_Rotenone7d_2 vs 3B_WT_untreated_2

hyb_protocol: 3B_WT_untreated_2 Cy5 / 4B_WT_Rotenone7d_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910135_b1 - 2C_WT_Rotenone12h_3 vs 4C_WT_Rotenone7d_3

hyb_protocol: 4C_WT_Rotenone7d_3 Cy5 / 2C_WT_Rotenone12h_3 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 254706910132_b4 - 4A_WT_Rotenone7d_1 vs 3A_WT_untreated_1

hyb_protocol: 3A_WT_untreated_1 Cy5 / 4A_WT_Rotenone7d_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Plasma, non-progressive, before FOLFIRINOX, sample 6 [6G, TIME 1]

city: Amsterdam

first: Elisa

last: Giovannetti

address: De Boelelaan 1117

department: Medical Oncology

country: Netherlands

institute: VUmc

description: 6G, TIME 1

data_processing:
All RT-PCR experiments and analysis were performed by Exiqon, Denmark. The amplification curves were analyzed using the Roche LC software, both for determination of Cq and for melting curve analysis. The amplification efficiency was calculated using algorithms similar to the LinReg software. Using NormFinder Software, the best normalizer was found to be the average of assays detect in all samples. All data was normalized to the average of assays detected in all samples: average detected in all samples - assay Cq value. The 'Matrix non-normalized' file contains the raw data for all samples as Cq values. MicroRNAs not detected are indicated by ND in the raw data sheet. The 'Matrix normalized' file contains the normalized data. A higher value thus indicates that the microRNA is more abundant in the particular sample. The 'Fold change' template contains the comparisons made between the groups. Three comparisons were made: before treatment expression of non-progressive compared to progressive patients (displayed in Fold change 1), after compared to before treatment of non-progressive patients (displayed in Fold change 2), and of progressive patients (displayed in Fold change 3). The Fold change was calculated by the equation of -2^-ddCt for down-regulated microRNAs and 2^ddCq for up-regulated microRNAs. A paired t-test was used to compare before and after treatment expression, unpaired t-test for non-progressive versus progressive.
Assays must be detected within 5 Cq values less than the negative control, and with Cq values < 37 to be included in the data analysis.

label: SYBR Green

organism: Homo sapiens

label_protocol: All experiments were conducted at Exiqon Services, Denmark. RNA was reverse transcribed using the miRCURY LNA Universal cDNA synthesis kit (Exiqon). cDNA was diluted ans assayed in PCR reactions according to the protocol for miRCURY LNA Universal RT microRNA PCR (Exiqon). MicroRNA expression was assessed on the microRNA Ready-to-Use PCR, Serum/Plasm focus panel using Exiqon SYBR Green Master Mix, including Negative controls. Amplification was performed in a Roche Lightcycler 480 Real-Time PCR system in a 384 wells plate.

extract_protocol: Total RNA was extracted from plasma using Exiqon's miRCURY Small RNA isolation Kit for Biofluids.

tag: sex (m/f)

value: F

tag: age

tag: histopathological diagnosis

value: Pancreatic ductal adenocarcinoma

tag: disease status

value: Non-progressive

tag: tumor stage

value: Stage IV

value: Plasma


title: Plasma, non-progressive, after FOLFIRINOX, sample 6 [6G, TIME 2]

description: 6G, TIME 2

source_name: Plasma_non-progressive_after FOLFIRINOX


title: Myc.Tgfa_14


title: Plasma, non-progressive, after FOLFIRINOX, sample 5 [5G, TIME 2]

description: 5G, TIME 2

value: M


title: Mei2-TAP tagged RIP

city: New York

first: Kaustav

last: Mukherjee

state: NY

address: 1 Gustave Levy Place

department: Cell, Developmental and Regenerative Biology

institute: Icahn School of Medicine at Mount Sinai

description: RNAs immunoprecipitated after 4h meiosis with Mei2-TAP

hyb_protocol: Labeled cDNAs were hybridized onto Agilent Comparative Genome Hybridization arrays for S. pombe (Agilent design ID: 020376 – see design format as a separate file) using an Agilent Gene Expression hybridization kit according to manufacturer’s instructions

scan_protocol: Hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner (part number G2505C). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

organism: Schizosaccharomyces pombe

source_name: yeast

label_protocol: Microarray Labeling and Hybridization was performed using a two-color Quick Amp Labeling Kit (Agilent) according to manufacturer’s instructions. RNAs after IP were labeled with Cy3 and the background probes were labeled with Cy5

growth_protocol: cells were grown on YES media with supplements at 30C till they reached log phase. They were then harvested, washed and put on ME media to induce meiosis. Samples were taken at 4,5,6 hours and pelleted. The pellet was washed with lysis buffer and flash frozen in liquid nitrogen and stored in -80C

extract_protocol: Pellets were thawed on ice, suspended in 400ul lysis buffer and lysed by bead beating using Zirconia beads. The lysate was clarified by centrifugation. After immunoprecipitation, RNA was extracted by phenol:chloroform extraction and ethanol precipitation

tag: tag

value: TAP

tag: mating type

tag: growth media

value: 4-6h in ME sporulation media

tag: sample type

value: IP

value: input


title: untagged negative control RIP

description: Negative control untagged Mei2


title: Plasma, non-progressive, before FOLFIRINOX, sample 5 [5G, TIME 1]

description: 5G, TIME 1


title: Myc.Tgfa_13


title: Plasma, non-progressive, before FOLFIRINOX, sample 3 [3G, TIME 1]

description: 3G, TIME 1


title: SV40_02

value: simian vacuolating virus 40 (SV40) T-antigen transgenic model


title: 254706910131_b2 - 2A_WT_Rotenone12h_1 vs 1A_WT_untreated_1

hyb_protocol: 1A_WT_untreated_1 Cy5 / 2A_WT_Rotenone12h_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Plasma, non-progressive, after FOLFIRINOX, sample 2 [New 2G, Time 2]

description: New 2G, Time 2


title: 254706910131_b3 - 1B_WT_untreated_2 vs 2B_WT_Rotenone12h_2

hyb_protocol: 2B_WT_Rotenone12h_2 Cy5 / 1B_WT_untreated_2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Myc.Tgfa_11


title: Myc.Tgfa_10


title: Plasma, non-progressive, before FOLFIRINOX, sample 2 [New 2G, Time 1]

description: New 2G, Time 1


title: Myc.Tgfa_12


title: Myc.Tgfa_06


title: Myc.Tgfa_07


title: Plasma, non-progressive, after FOLFIRINOX, sample 1B [New 1G, Time 2]

description: New 1G, Time 2


title: Myc.Tgfa_08


title: Plasma, non-progressive, before FOLFIRINOX, sample 1B [New 1G, Time 1]

description: New 1G, Time 1


title: Myc.Tgfa_09


title: 254706910131_b1 - 1A_WT_untreated_1 vs 2A_WT_Rotenone12h_1

hyb_protocol: 2A_WT_Rotenone12h_1 Cy5 / 1A_WT_untreated_1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Plasma, non-progressive, after FOLFIRINOX, sample 1A [Res 1G,time2]

description: Res 1G,time2

value: Stage III


title: Plasma, progressive, after FOLFIRINOX, sample 6 [6B, TIME 2]

description: 6B, TIME 2

source_name: Plasma_progressive_after FOLFIRINOX

value: Progressive


title: Myc.Tgfa_05


title: Plasma, progressive, after FOLFIRINOX, sample 5 [5B, TIME 2]

description: 5B, TIME 2


title: Plasma, progressive, before FOLFIRINOX, sample 6 [6B, TIME 1]

description: 6B, TIME 1

source_name: Plasma_progressive_before FOLFIRINOX


title: Myc.Tgfa_04


title: Plasma, progressive, before FOLFIRINOX, sample 5 [5B, TIME 1]

description: 5B, TIME 1


title: Plasma, progressive, after FOLFIRINOX, sample 4 [4B, TIME 2]

description: 4B, TIME 2


title: Myc.Tgfa_01


title: Myc.E2f1_15

value: transgenic mice expressing Myc/E2f15


title: Myc.Tgfa_03

value: transgenic mice expressing Myc/transforming growth factor alpha (Tgfa)


title: Plasma, progressive, before FOLFIRINOX, sample 4 [4B, TIME 1]

description: 4B, TIME 1


title: Plasma, non-progressive, before FOLFIRINOX, sample 1A [Res 1G,time1]

description: Res 1G,time1


title: Myc.E2f1_13

value: transgenic mice expressing Myc/E2f13

value: liver


title: Plasma, progressive, after FOLFIRINOX, sample 3 [3B, TIME 2]

description: 3B, TIME 2

value: F


title: Myc.E2f1_14

value: transgenic mice expressing Myc/E2f14


title: Myc.E2f1_12

value: transgenic mice expressing Myc/E2f12


title: Plasma, progressive, after FOLFIRINOX, sample 2 [2B, TIME 2]

description: 2B, TIME 2

value: Pancreatic ductal adenocarcinoma

value: Stage IV


title: Plasma, progressive, before FOLFIRINOX, sample 2 [2B, TIME 1]

description: 2B, TIME 1

value: M

value: Plasma


title: Plasma, progressive, before FOLFIRINOX, sample 3 [3B, TIME 1]

description: 3B, TIME 1


title: Myc.Tgfa_02


title: Myc.E2f1_09

value: transgenic mice expressing Myc/E2f9


title: Myc.E2f1_10

value: transgenic mice expressing Myc/E2f10


title: 5dpa_WE_3

type: SRA

city: Cambridge

first: Douglas

middle: A.

last: Melton

state: MA

address: 7 Divinity Ave.

institute: Harvard University

description:
kallisto_counts_matrix.TMM.EXPR.matrix.tab
Two instrument models:  Illumina Hiseq 2500 and Nextseq 500

library_source: transcriptomic

data_processing:
Samples were sequenced on one run of the Ilumina Nextseq 500 (300 cycle) and across 6 lanes of the Illumina Hiseq 2500 (raw read files for Hiseq were concatenated for ease of uploading).
The reads were aligned to a previously generated annotated axolotl de novo transcriptome (Bryant et al., 2017, GEO accession GSE92429). Alignment of samples and normalized TPMs were generated using Kallisto software (https://pachterlab.github.io/kallisto/) according to default parameters.
Differential expression analysis was performed using DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: GFBM000000000.1
Supplementary_files_format_and_content: tab delimited text file containing the normalized counts (TMM-normalized TPMs) for all samples (27 columns) for each transcript in the transcriptome (rows)

organism: Ambystoma mexicanum

source_name: 5 dpa WE

extract_protocol:
Intact or regenerating limb tissue was microdissected into stump or epithelium fractions. Each fraction was chemically dissociated with either Trypsin-EDTA (epidermis) or collagenase/dispase (stump tissues). Each fraction was then stained with 10 ug/ml of DAPI. Stump tissues were then FACS sorted for 2N and 4N fractions. RNA was then isolated from all three fractions (stump 2N, stump 4N, and epidermis) using the Recoverall Total Nucleic Acid Isolation Kit for FFPE (Invitrogen). RNA quality was assessed on the Bioanalyzer 2100.
cDNA was generated using 10 ng of RNA input for the NuGEN Ovation RNA-seq System V2 protocol (Integrated Sciences). The quality and concentration of cDNA preps was then assessed using the Agilent DNA 1000 kit on the Bioanalyzer 2100 (Agilent Technologies). To prepare cDNA sequencing libraries, cDNA was first sheared to a peak size of 200 bp using the Covaris S220 (Covaris, Woburn, MA) according to the manufacturer’s protocol. Good quality and correct size distribution of sheared DNA fragments was assessed with the Agilent DNA High Sensitivity kit on the Bioanalyzer 2100 (Agilent Technologies). Sequencing libraries were then generated using the Wafergen PrepX Complete ILMN DNA Library kit (Takara Bio) protocol on the Apollo 324 NGS Library Prep System (Takara Bio). Quality of the DNA sequencing libraries was performed with the Agilent DNA High Sensitivity kit on the Bioanalyzer 2100 (Agilent Technologies).

value: Axolotl limb (regenerating)

tag: cellular fraction

value: wound epidermis

tag: time

value: 5 days post-amputation (dpa)


title: Myc.E2f1_11

value: transgenic mice expressing Myc/E2f11


title: Myc.E2f1_06

value: transgenic mice expressing Myc/E2f6


title: Myc.E2f1_04

value: transgenic mice expressing Myc/E2f4


title: Myc.E2f1_07

value: transgenic mice expressing Myc/E2f7


title: Myc.E2f1_08

value: transgenic mice expressing Myc/E2f8

value: liver


title: 5dpa_4N_3

source_name: 5 dpa 4N


title: 5dpa_4N_2


title: KD2

city: Tianjin

first: Yuanjie

last: Niu

address: Pingjiang Road 23

country: China

institute: Tianjin Institute of Urology

description: All_Differentially_Expressed_Transcripts

data_processing:
Basecalls performed using Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8)
RNA-seq reads were aligned to the HG19 genome assembly using Hisat2 (v2.0.4)
Software Ballgown was used to calculate the FPKM.
Genome_build: HG19
Supplementary_files_format_and_content: Excel file with FPKM and statistical analysis

source_name: LNCaP-AI cells transfected with lncRNA PCAT1 shRNA

growth_protocol: The parental androgen dependent human prostate cancer cell line LNCaP were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA).For androgen deprivation，parental LNCaP cells were maintained in RPMI 1640 medium supplemented with 10% charcoal-stripped fetal bovine serum (BI, Cromwell, CT, USA). Cells were incubated at 37 °C with 5% CO2.

extract_protocol:
Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).
Libraries were prepared according to instructions accompanying theNEB_NEBNext® Poly(A) mRNA Magnetic Isolation Module, Illumina(Epicentre)_RiboZero Magnetic Gold Kit(Human/Mouse/Rat), KAPA_ Stranded RNA-Seq Library Prep Kit（Illumina）

treatment_protocol: The LNCaP-AI line was generated following long-term culture of the parental LNCaP cells under androgen deprived conditions.

tag: cell line

value: LNCaP-AI

tag: transfected with

value: lncRNA PCAT1 shRNA


title: Myc.E2f1_02

tag: genotype/variation

value: transgenic mice expressing Myc/E2f2


title: 5dpa_4N_1

tag: tissue


title: HCAEC-negative control siRNA

city: Guangzhou

first: Liu

last: Benrong

address: No.250 Changgang Dong Road

institute: Guangzhou institute of cardiovascular disease

description: Gene expression at 72 hours after transfection with negative control siRNA

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: HCAEC, negative control siRNA, 72 hr

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: The human coronary artery endothelial cells (HCAEC) were cultured in EGM-2 medium (Lonza, USA) supplemented with 2% (v/v) fetal bovine serum (FBS), 0.2 ml of hydrocortisone, 2 ml of FGF-B, 0.5 ml of VEGF, 0.5 ml of R3-IGF-1, 0.5 ml of ascorbic acid, 0.5 ml of hEGF, 0.5 ml GA-1000 and 0.5 ml of HEPARIN, and were grown at 37 ℃ in a humidified atmosphere with 5% (v/v) CO2. It was passaged according to 1:3 when the cells reached approximately 85-95% confluence.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The siRNA and Negative control were diluted to 20 μM solution with RNASE free and sterile deionized water, and stored at < -20℃. HCAEC were seeded in a plate at a density of 7500 cells/cm2 at 18-24 hours before transfection, and were cultured at 37 ℃ in a humidified atmosphere with 5% (v/v) CO2. Lipofectamine® RNAiMAX reagent was used to guide siRNA into cells, and the procedure was performed according to the manufacturer’s instructions. The final concentration of siRNA was 40 nM in each well.

tag: cell type

value: human cronary artery endothelial cell

tag: transfection

value: negative control siRNA


title: Myc.E2f1_03

value: transgenic mice expressing Myc/E2f3


title: KD1


title: Myc.E2f1_05

value: transgenic mice expressing Myc/E2f5


title: E2f1_17

value: transgenic mice expressing E2F transcription factor 1 (E2f1)


title: C3

source_name: LNCaP-AI cells transfected with scramble shRNA

value: scramble shRNA


title: Myc.E2f1_01

value: transgenic mice expressing Myc/E2f1


title: E2f1_16


title: 5dpa_2N_3

source_name: 5 dpa 2N

value: Axolotl limb (regenerating)

value: 5 days post-amputation (dpa)


title: HCAEC-siMEF2A-rep2

description: Gene expression at 72 hours after transfection with MEF2A specific siRNA

source_name: HCAEC, MEF2A specific siRNA, 72 hr

value: MEF2A specific siRNA


title: 5dpa_WE_1

value: wound epidermis


title: KD3


title: HCAEC-siMEF2A-rep3


title: C2


title: HCAEC-siMEF2A-rep1


title: 5dpa_WE_2


title: 5dpa_2N_2


title: E2f1_18


title: C1


title: U13

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

country: Sweden

institute: Lund Univeristy

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials â€¢ Heat cocktails at 99Â° for 5 minutes, then 42Â° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). â€¢ Transfer 200Î¼l of hyb solution to each array, then tape holes and parafilm. â€¢ Hybridize 16 hours at 45Â° at 60rpmâ€¢ Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using Bioconductor R package Affy. Labeling batches were combined and normalized using RMA.

label: biotin

source_name: Nephroureterectomy

label_protocol: Sensation Plus labeling and amplification kit, according to Manufacturers (Affymetrix) protocols.

extract_protocol: High Pure FFPET RNA isolation kit (Roche)

tag: pt

tag: anatomical site

value: Renal pelvis

tag: tumor grade (who 1999)

tag: msi-status

value: MSS


title: 5dpa_2N_1


title: SV40_09

value: simian vacuolating virus 40 (SV40) T-antigen transgenic model

value: liver


title: U32

source_name: Nefroureterectomy

value: MSI-L


title: 4dpa_WE_2

source_name: 4 dpa WE

value: 4 days post-amputation (dpa)


title: E2f1_14


title: Bla16

source_name: Transurethral excision, bladder

value: Bladder


title: 4dpa_WE_1


title: E2f1_15


title: E2f1_12


title: 4dpa_4N_3

source_name: 4 dpa 4N


title: 4dpa_4N_2


title: KONC_MEF

city: Minhang

first: bing

last: zhang

state: Shanghai

address: 800 Dong Chuan Road

department: Shanghai Center for Systems Biomedicine

institute: Shanghai Jiao Tong University

description: RNA-seq on wild-type MEFs

data_processing:
Raw reads were filtered using Cutadapt (https://cutadapt.readthedocs.io/en/stable/) and checked by FastQC.
Filtered reads were mapped to GRCh37 using STAR with GENCODE19 annotation. Mapped reads in each gene were counted using GFOLD (https://bitbucket.org/feeldead/gfold) with default setting
Gene expression changes were quantified using GFOLD diff, with which the calculation was based on the posterior distribution of log fold change. A threshold of “|GFOLD|≥0.585” was set to select differential expressed genes.
Genome_build: GRCh37
Supplementary_files_format_and_content: RPKM

source_name: MEF

growth_protocol: MDA-MB-231 cells provided by Dr. Sean Li (Harvard University) were grown in L-15 medium (Gibco) and 10% fetal bovine serum. HCC1937 cells purchased from Cell Bank of Shanghai Institutes for Biological Sciences were grown in RPMI 1640 medium (Gibco) supplemented with NaHCO3 1.5 g/L, glucose 2.5 g/L, Sodium Pyruvate 0.11 g/L, and 10% fetal bovine serum. MEF cells were purified from LARP7+/+ or LARP7-/-  embryos at the age of E13.5 and used for experiments with passages between 1-6,  and were cultured in DMEM with 10% fetal bovine serum.

extract_protocol:
Total RNA was purified by using RNeasy miniprep kit (Qiagen) with an on-column DNAseI digestion protocol to eliminate the residual DNA.
RNA-seq protocol followed NEBNext® UltraTM RNA library Prep Kit for Illumina (NEB).

treatment_protocol: For siRNA experiment, 10ng/ml siRNA was used.

value: MEF

value: wild-type


title: siNC_231

description: RNA-seq on MDA-MB-231 with siNC treatment

tag: sirna

value: siNC


title: siNC_HCC1937

description: RNA-seq on HCC1937 with siNC treatment


title: 4dpa_WE_3


title: siLP7_HCC1937

description: RNA-seq on HCC1937 with siLARP7 treatment


title: KOLP7_MEF

description: RNA-seq on LARP7-/- MEFs


title: U15

value: MSI-H


title: E2f1_13

source_name: HCC tumor

value: transgenic mice expressing E2F transcription factor 1 (E2f1)


title: Bla10

source_name: TUR-B

value: pTa


title: Bla7


title: E2f1_10


title: E2f1_09


title: 4dpa_4N_1

value: Axolotl limb (regenerating)


title: siLP7_231

description: RNA-seq on MDA-MB-231 with siLARP7 treatment


title: Mutant TDP-43 (N352S, homozygous) 82

city: La Jolla

first: Don

middle: W

last: Cleveland

state: CA

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

data_processing:
50bp single-end FASTQ files were obtained using the Illumina demultiplexing pipeline. STAR (Dobin et al., 2013) and RSEM (Li and Dewey, 2011) were used to align the reads to the human reference sequence HG38 and to calculate the raw counts and transcripts per million (TPM) values for genes, respectively
Genome_build: HG38
Supplementary_files_format_and_content: TPM, csv format

source_name: SH-SY5Y cell line

growth_protocol: The neuroblastoma cells (ATCC) were cultured in DMEM/F12 (Gibco) supplemented with 10% fetal-bovine serum (Omega) and 1% penicillin-streptomycin (Gibco) at 37 °C with 5% CO2.

extract_protocol:
For RNA extraction, direct lysis was applied using Trizol reagent (Invitrogen) and RNA was purified according to the manufacturer’s instructions.
Illumina TruSeq RNA kit

treatment_protocol: For knockdown experiments, cells were transfected with SMARTpool ON-TARGETplus siRNA targeting TDP-43 (L-012394) or control siRNA pool (D001810-10) (GE Dharmacon) at final concentration of 50nM, for 96 hours in two doses (0, 24h), after complexing with Lipofectamin RNAiMAX (Invitrogen) in Opti-MEM (Gibco) for 20 minutes.

value: Mutant TDP-43


title: Bla3


title: E2f1_08


title: 4dpa_2N_3

source_name: 4 dpa 2N


title: Bla5

source_name: Total cystectomy


title: U22

value: Ureter


title: U30


title: E2f1_11


title: E2f1_07


title: U26


title: Mutant TDP-43 (N352S, homozygous) 81


title: Plasma, non-progressive, after FOLFIRINOX, sample 3 [3G, TIME 2]

description: 3G, TIME 2

source_name: Plasma_non-progressive_after FOLFIRINOX

tag: sex (m/f)

value: M

tag: age

tag: histopathological diagnosis

value: Pancreatic ductal adenocarcinoma

tag: disease status

value: Non-progressive

tag: tumor stage

value: Stage IV

value: Plasma


title: 4dpa_2N_1

tag: cellular fraction

tag: time


title: TDP-43 wild type 80

value: wild type


title: TDP-43 wild type 79


title: 0dpa_epi_3

source_name: 0 dpa epi

value: Axolotl limb (intact)

value: normal epidermis

value: 0 days post amputation (dpa)


title: 4dpa_2N_2

value: 4 days post-amputation (dpa)


title: siTDP-43 3

tag: treatment


title: 0dpa_epi_2


title: siTDP-43 2


title: siTDP-43 1


title: 0dpa_epi_1


title: E2f1_06

tag: genotype/variation

value: liver


title: E2f1_05

tag: tissue


title: 0dpa_4N_3

source_name: 0 dpa 4N


title: U2

value: Renal pelvis

value: MSS


title: E2f1_03

value: transgenic mice expressing E2F transcription factor 1 (E2f1)


title: U24

value: MSI-H


title: E2f1_04


title: Bla13

value: Bladder

value: MSI-L


title: siControl 3

value: siControl


title: 0dpa_4N_2


title: 0dpa_4N_1


title: E2f1_02


title: 0dpa_2N_3

source_name: 0 dpa 2N


title: U10


title: E2f1_01


title: siControl 1


title: Myc_15

value: transgenic mice expressing myelocytomatosis oncogene (Myc)


title: Bla21

source_name: Biopsy

value: pTa


title: U14

source_name: Excisio tumor

value: Ureter


title: U36

source_name: Nephroureterectomy


title: U23


title: Myc_14


title: intron-DARP-EGFP line scrambled siRNA replicate 6

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

description:
SUPT4H1_HEK293_intron.tab.gz
scramble_6

data_processing:
Sequencing adapters were trimmed using skewer (Jiang et al., 2014; version 0.2.2) with default parameters. Quality control of the trimmed reads was performed using FastQC (version 0.11.5: www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were aligned to a composite index of the human genome (version GRCh38_p10) and sequences of the 92 ERCC spike-in transcripts: A STAR index (Dobin et al., 2013; version 2.5.3a) was built with the --sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release 27) were provided via the --sjdbGTFfile argument. STAR alignments were generated with the following parameters: --outFilterType BySJout --quantMode TranscriptomeSAM --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM MD XS --outSAMunmapped Within. Post-alignment quality control reports were generated using MultiQC (Ewels et al., 2016; version 1.0).
The raw gene expression matrix was constructed from the 'forward' column of STAR's ReadsPerGene.out.tab output files using R (version 3.4.3). Gene symbols and Entrez gene identifiers were mapped using Ensembl (version 86) via the biomaRt R package (Durinck et al, 2009; version 2.34.0).
GRCh38
Genome_build: tab-delimited, gzip-compressed text file with matrix of raw quantitation results for each sample.

source_name: Human embryonic kidney

growth_protocol: HEK293 CRL-1573 (ATCC) cells were cultured in DMEM, 10% FBS, 100 units/ml penicillin and streptomycin, 37 deg.C, 5% carbon dioxide, 100% humidity

extract_protocol:
72 hours post transfection, total RNA was extracted with the RNEasy (Qiagen) kit from 1,000,000 cells per sample.  Either ERCC mix1 or mix2 external standards (Invitrogen) were diluted 1:100 in water and 2 ul was added to each lysate.
Sequencing libraries were generated using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen).   200 ng RNA was used for library preparation for each sample.

treatment_protocol: Cells were transfected at 50% confluency in 6-well plates by combining either SUPT4H1 siRNA or scramble siRNA with 9 ul of RNAi max transfection reagent (Invitrogen) at a final concentration of 100 nM in a total volumne of 1.3 ml.

tag: cell line

tag: reporter

value: endogenous intronic sequence + DARP

tag: exogenous gene expressed

value: DARP-EGFP

value: scrambled siRNAs

tag: ercc mix

tag: hours post-infection

value: 72 hours

tag: rin

tag: replicate


title: 0dpa_2N_2

value: Axolotl limb (intact)

value: 0 days post amputation (dpa)


title: siControl 2


title: Myc_13

value: liver


title: 0dpa_2N_1


title: intron-DARP-EGFP line scrambled siRNA replicate 5

description:
SUPT4H1_HEK293_intron.tab.gz
scramble_5


title: intron-DARP-EGFP line scrambled siRNA replicate 3

description:
SUPT4H1_HEK293_intron.tab.gz
scramble_3


title: Bla4

tag: pt

tag: anatomical site

tag: tumor grade (who 1999)

tag: msi-status


title: Myc_10


title: Bla6


title: Myc_12


title: Myc_11


title: Bla8


title: EPS-17: Mn rep2

city: Nashville

first: Eric

last: Skaar

state: TN

address: 1161 21st Avenue South, Medical Center North A5102

department: Department of Pathology, Microbiology, and Immunology

institute: Vanderbilt University Medical Center

data_processing:
CLC Genomics workbench (version 11.0.1, Qiagen) was used for base calling.
CLC Genomics workbench (version 11.0.1, Qiagen) was used for adapter, quality trimming, and alignment.
CLC Genomics workbench (version 11.0.1, Qiagen) was used for data analysis
Genome_build: NC_009641
Supplementary_files_format_and_content: RNA abundance

organism: Staphylococcus aureus subsp. aureus str. Newman

source_name: Bacterial cells

growth_protocol: S. aureus WT strains were streaked onto TSA and incubated at 37 °C for 24 h. Single colonies were selected in biological triplicate and used to inoculate 5 ml of TSB. Cultures were grown for 15 h at 37 °C.  Cultures were back-diluted 1:100 in 5 ml TSB and grown at 37 C until mid-log phase. Cultures were centrifuged, the supernatant removed, and the cell pellets resuspended in TSB.

extract_protocol:
RNA was isolated using Tri reagent and chloroform and precipitated with isopropanol. RNA was isolated using the Qiagen RNeasy Mini Kit. Precipitated RNAs were treated with DNase I (ThermoFisher) following the manufacturer’s instructions.
rRNA was depleted using the Ribo-Zero rRNA Removal Kit (Bacteria) (Epicentre) and paired-end cDNA libraries prepared with a TruSeq RNA Library Prep Kit v2 (Illumina).
RNA sequencing was performed by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core using the Illumina HiSeq 3000 platform (Illumina)

treatment_protocol: Equal volumes of the resuspended cultures were added to TSB or TSB supplemented with MnCl2 (final concentration of 1 mM MnCl2). Cells were incubated for 30 min at 37 °C, centrifuged, and the remaining cell pellet subjected to RNA extraction.

tag: strain

value: Newman

value: TSB + 1 mM MnCl2

value: Bacterial cells


title: Myc_08


title: Myc_09


title: intron-DARP-EGFP line scrambled siRNA replicate 2

description:
SUPT4H1_HEK293_intron.tab.gz
scramble_2


title: Bla1

source_name: Transurethral excision, bladder


title: intron-DARP-EGFP line scrambled siRNA replicate 4

description:
SUPT4H1_HEK293_intron.tab.gz
scramble_4


title: EPS-16: Mn rep1


title: EPS-18: Mn rep3


title: Bla15

value: MSS


title: EPS-15: Untreated rep3

value: TSB


title: intron-DARP-EGFP line scrambled siRNA replicate 1

description:
SUPT4H1_HEK293_intron.tab.gz
scramble_1


title: intron-DARP-EGFP line SUPT4H1 siRNA replicate 6

description:
SUPT4H1_HEK293_intron.tab.gz
SUPT4H1_6

value: SUPT4H1 siRNAs


title: EPS-14: Untreated rep2


title: intron-DARP-EGFP line SUPT4H1 siRNA replicate 5

description:
SUPT4H1_HEK293_intron.tab.gz
SUPT4H1_5


title: U1

source_name: excisio tumor (biopsy)


title: Myc_06


title: EPS-13: Untreated rep1


title: Bla19

value: Bladder


title: intron-DARP-EGFP line SUPT4H1 siRNA replicate 4

description:
SUPT4H1_HEK293_intron.tab.gz
SUPT4H1_4


title: intron-DARP-EGFP line SUPT4H1 siRNA replicate 3

description:
SUPT4H1_HEK293_intron.tab.gz
SUPT4H1_3


title: Myc_04

value: transgenic mice expressing myelocytomatosis oncogene (Myc)


title: U28

value: pTa

value: Renal pelvis


title: intron-DARP-EGFP line SUPT4H1 siRNA replicate 2

description:
SUPT4H1_HEK293_intron.tab.gz
SUPT4H1_2

value: endogenous intronic sequence + DARP


title: Myc_05


title: MoM_20B

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: Periacetabular synovial tissue

extract_protocol:
Tissues were immediately snap-frozen in liquid nitrogen and stored at -80C until mRNA isolation. Frozen biopsy samples were pulverized into powder using a cold mortar and pestle. Crushed samples were then placed into Qiazol reagent and homogenized using the TissueLyser LT (Qiagen, Hilden, Germany). Genomic RNA extractions were performed using the miRNeasy mini kit (Qiagen, Venlo, Netherlands) according to the manufacturer's protocol.The Mayo Clinic Gene Expression Core (Advanced Genomics Technology Center, Mayo Clinic, Rochester, MN) provided RNA integrity (RIN) scores for prioritization of samples best suited to RNA-seq data acquisition
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tha status

value: Revision

tag: cell type

value: Fibroblast

value: hip capsular tissue

tag: status

value: metal

tag: exposure

value: cobalt chromium exposed tissue


title: Bla14


title: Bla17


title: U37

source_name: Nefroureterectomy

value: Ureter


title: Myc_02

source_name: HCC tumor

tag: genotype/variation

tag: tissue

value: liver


title: Patient_343

city: Berlin

first: Henrik

last: Seidel

address: Muellerstr. 178

country: Germany

institute: Bayer AG

data_processing: Normalized continous values were calculated with an in-house developed algorithm for all miRNAs detected in at least 50% of samples, values below detection threshold were imputed. Dichotomized values (1 / 0 for detected / not detected) were calculated for all miRNAs detected in less than 50% of samples.

source_name: plasma

label_protocol: 18 μl of purified total RNA was reverse transcribed in 90-μL-reactions using the Universal cDNA Synthesis Kit II and the UniSP6 spike-in (Exiqon). Conditions for reverse transcription reaction were incubation at 42°C for 60 minutes followed by five minutes at 95°C. The resulting cDNA was subsequently diluted 60 times in the ExiLENT SYBR® Green master mix (Exiqon) and assayed in 10 μL reactions according to the manufacturer's instruction. As inter-plate calibrator we used UniSP3 oligonucleotide. Relative quantitative real-time PCR was performed using the HT7900 (Applied Biosystems). RT-PCR conditions were incubation at 95°C for 10 minutes followed by 45 cycles of 95°C for 10 seconds and 60°C for one minute.

extract_protocol: RNA was isolated from plasma using the mirCury RNA isolation kit (Exiqon)

treatment_protocol: untreated (baseline expression)

tag: arm

value: Regorafenib 160 mg

tag: os

tag: ttp

tag: batch

tag: unisp2 outlier

value: FALSE

tag: unisp4 outlier

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo

tag: hemo status

value: good


title: MoM_9B


title: U33

tag: pt

tag: anatomical site

tag: tumor grade (who 1999)

tag: msi-status

value: MSI-L


title: pTHA_38A

tag: tha status

value: Primary

tag: cell type

tag: status

value: metal-naïve

tag: exposure

value: non-exposed tissue


title: pTHA_23A

tag: tissue


title: pTHA_33A


title: Patient_339

tag: arm

tag: os

tag: ttp


title: Patient_338

value: Placebo

tag: batch

tag: unisp2 outlier

tag: unisp4 outlier


title: Patient_342

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo


title: Patient_340

tag: hemo status

value: medium


title: Patient_341


title: Patient_337


title: Myc_03

tag: genotype/variation

value: transgenic mice expressing myelocytomatosis oncogene (Myc)


title: Myc_07


title: Patient_336


title: U17

tag: pt

tag: anatomical site

tag: tumor grade (who 1999)

tag: msi-status

value: MSS


title: Patient_334


title: DEN_15

value: diethylnitrosamine (DEN)-induced model


title: DEN_14


title: Patient_335


title: Bla11

source_name: TUR-B

value: Bladder


title: DEN_09


title: U34

source_name: Partial Ureterectomy


title: DEN_16


title: U5

source_name: Biopsy from  ureter

value: pTa


title: Patient_333


title: U11

value: Renal pelvis


title: Bla2


title: DEN_08


title: U16

value: Ureter

value: MSI-H


title: U29

source_name: Resection of neoureter


title: DEN_07

value: liver


title: DEN_11


title: Patient_332

value: Regorafenib 160 mg

value: FALSE


title: U6


title: Patient_331

value: good


title: DEN_12


title: DEN_13


title: Patient_330


title: DEN_06


title: Bla12


title: HF RV 5w biological replicate 3

city: Philadelphia

first: Mariana

middle: Alejandra

last: Argenziano

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Human Genetics

institute: Children's Hospital Of Philadelphia

description: Gene expression data

hyb_protocol: The amplified RNA was purified with magnetic beads, and 15 μg Biotin-aRNA was fragmented with fragmentation reagent. 12.5 μg fragmented aRNA was hybridized to Thermo Fisher Scientific Canine Genome 2.0 arrays along with hybridization cocktail solution and then placed in GeneChip Hybridization Oven 645 (Thermo Fisher Scientific) rotating at 60 rpm at 45ºC for 16 h

scan_protocol: The chips were scanned with Thermo Fisher Scientific GeneChip Scanner 30007G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Canis lupus familiaris

source_name: Late heart failure right ventricle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from  total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Dogs were ventricular tacghypaced for 2 weeks (early HF) or 5 weeks (late HF)

extract_protocol: After euthanasia, a small piece of tissue was isolated from each chamber and snap frozen for RNA isolation and subsequent transcriptomic characterization prior to electrophysiologic study

treatment_protocol: To produce “early” and “late” stages of HF, adult mongrel or beagle dogs were continuously paced using a modified Medtronic (Minneapolis, Minnesota) pacemaker for a period of 2-3 and 5-6 weeks, respectively

value: right ventricle

tag: condition

value: late heart failure

value: heart


title: DEN_10

tag: tissue


title: DEN_05


title: Patient_329

tag: arm


title: intron-DARP-EGFP line SUPT4H1 siRNA replicate 1

description:
SUPT4H1_HEK293_intron.tab.gz
SUPT4H1_1

tag: cell line

tag: reporter

value: endogenous intronic sequence + DARP

tag: exogenous gene expressed

value: DARP-EGFP

tag: treatment

value: SUPT4H1 siRNAs

tag: ercc mix

tag: hours post-infection

value: 72 hours

tag: rin

tag: replicate


title: HF RV 5w biological replicate 2

description: Gene expression data


title: Patient_328

tag: os

tag: ttp

tag: batch

tag: unisp2 outlier

tag: unisp4 outlier

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo

tag: hemo status

value: medium


title: MoM_14B

tag: tha status

value: Revision

tag: cell type

value: Fibroblast

tag: tissue

value: hip capsular tissue

tag: status

value: metal

tag: exposure

value: cobalt chromium exposed tissue


title: HF RV 5w biological replicate 1

description: Gene expression data

tag: condition


title: ST3 hESC-derived MHC-mCheery- cells-2

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina CASAVA v1.8.4 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome using STAR v2.5.2b.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file including gene name, Ensembl id, locus, RPKM values for each gene in each sample

source_name: MYH6:mCherry hESC reporter line

extract_protocol:
RNA was prepared from sorted cells with Absolutely RNA Nanoprep kit. The cDNA libraries were generated using TruSeq RNA Sample Preparation (Illumina). Each library was sequenced using single-end reads in the HiSeq4000 format (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell subtype

value: MHC-mCheery-

tag: differentiation time point

value: cardiac differentiation day20

value: hESCs


title: ST4 hESC-derived MHC-mCheery+ cells-2

value: MHC-mCheery+


title: DEN_04

tag: genotype/variation

value: diethylnitrosamine (DEN)-induced model

value: liver


title: DEN_03


title: HF RV 2w biological replicate 3

description: Gene expression data

source_name: Early heart failure right ventricle

value: right ventricle

value: early heart failure

value: heart


title: Patient_327

tag: arm

value: Regorafenib 160 mg

tag: os

tag: ttp

value: FALSE

value: bad


title: DEN_01


title: DEN_02


title: ST2 hESC-derived MHC-mCheery+ cells-1


title: Myc_01

value: transgenic mice expressing myelocytomatosis oncogene (Myc)


title: HF RV 2w biological replicate 2

description: Gene expression data


title: ST1 hESC-derived MHC-mCheery- cells-1


title: Patient_326

tag: batch

tag: unisp2 outlier

tag: unisp4 outlier

value: good


title: HF RV 2w biological replicate 1

description: Gene expression data


title: Patient_325

value: Placebo

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo


title: Patient_323

tag: hemo status


title: Patient_324


title: HF RA 5w biological replicate 3

description: Gene expression data

source_name: Late heart failure right atria

tag: tissue

value: right atria

value: late heart failure


title: Patient_322


title: Patient_321


title: HF RA 5w biological replicate 2

description: Gene expression data


title: HF RA 5w biological replicate 1

description: Gene expression data


title: Patient_319


title: Patient_320


title: HF RA 2w biological replicate 3

description: Gene expression data

source_name: Early heart failure right atria


title: HF RA 2w biological replicate 1

description: Gene expression data


title: Patient_318


title: Patient_317


title: HF RA 2w biological replicate 2

description: Gene expression data


title: CONTROL RV biological replicate 1

description: Gene expression data

source_name: Control right ventricle

value: control


title: CONTROL RV biological replicate 3

description: Gene expression data


title: CONTROL RA biological replicate 3

description: Gene expression data

source_name: Control right atria


title: CONTROL RA biological replicate 1

description: Gene expression data


title: CONTROL RA biological replicate 2

description: Gene expression data


title: CONTROL RV biological replicate 2

description: Gene expression data


title: Plasmablast – Mzb1 ko – Replicate 2

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Plasmablast – Mzb1 ko – Replicate 2

data_processing:
The base calling was performed by using BCL2Fastq pipeline (version: 0.3.1) and bcl2fastq (version 2.17.1.14).
The paired-end RNA-Seq datasets were mapped to the mouse reference genome (mm9) using Tophat (v2.0.14)
The mapped reads were further assembled by using Cufflinks (v2.2.1) and the expression level of the annotated genes (UCSC, mm9) was calculated by Cuffquant
The differential gene expression between the conditions was calculated by using Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: The normalized gene expression values (FPKM) calculated by Cuffnorm (v2.2.1) is provided in TXT format

source_name: CD138+ Blimp1-GFP+ cells

growth_protocol: Splenic B cells were purified using anti-B220 magnetic beads and cultured in the presence of LPS for 4 days in IMDM Medium (12440-053-Gibco) in 10% FCS.

extract_protocol:
Total RNA was isolated from sorted in vitro differentiated Act B, Pre-PB and PB cells using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. The total mRNA was enriched by using Oligo dT magnetic beads.
The libraries were prepared by using TruSeq® Stranded mRNA library preparation protocol according to the manufacturer's instructions.

treatment_protocol: The cells were treated with 25ug/ml LPS (L5668-Sigma) and after 4 days cells were sorted with a FACSAria (Becton Dickinson) as Act B (CD138-Blimp1-GFP-), Pre-PB (CD138-Blimp-GFP+) and PB (CD138+Blimp-GFP+) cells, using CD138 antibody (BD).

tag: strain

value: Spleen

tag: genotype

value: Mzb1-/- Prdm1+/gfp

tag: cell type

value: Plasmablast


title: Plasmablast – Mzb1 ko – Replicate 1

description: Plasmablast – Mzb1 ko – Replicate 1


title: Plasmablast – Mzb1 wt – Replicate 2

description: Plasmablast – Mzb1 wt – Replicate 2

value: Mzb1+/+ Prdm1+/gfp


title: Patient_315


title: Plasmablast – Mzb1 wt – Replicate 1

description: Plasmablast – Mzb1 wt – Replicate 1


title: Patient_316


title: Patient_314


title: Patient_313


title: pre-Plasmablast – Mzb1 ko – Replicate 2

description: pre-Plasmablast – Mzb1 ko – Replicate 2

source_name: CD138- Blimp1-GFP+ cells

value: pre-Plasmablast


title: pre-Plasmablast – Mzb1 ko – Replicate 1

description: pre-Plasmablast – Mzb1 ko – Replicate 1


title: pre-Plasmablast – Mzb1 wt – Replicate 2

description: pre-Plasmablast – Mzb1 wt – Replicate 2


title: Patient_311


title: pre-Plasmablast – Mzb1 wt – Replicate 1

description: pre-Plasmablast – Mzb1 wt – Replicate 1


title: Patient_308


title: Patient_310


title: Patient_312

value: medium


title: Patient_309


title: Activated B cells – Mzb1 ko – Replicate 2

source_name: CD138- Blimp1-GFP- cells

value: Activated B cells


title: Activated B cells – Mzb1 ko – Replicate 1


title: Activated B cells – Mzb1 wt – Replicate 1


title: Patient_307


title: Activated B cells – Mzb1 wt – Replicate 2


title: Patient_306


title: Patient_305


title: Patient_304


title: Patient_302


title: Patient_303


title: Patient_301


title: primary melanocyte C230_2

type: genomic

city: Rockville

first: Tongwu

last: Zhang

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

description: Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-24-v1-1_a Genotyping BeadChips (Illumina)

hyb_protocol: Resuspended samples are denatured, then hybridized to locus-specific 50-mer oligonucleotides which are attached to 1-micron beads on the BeadChip.  These 50-mer probes stop one base before the location of interest.  Enzymatic single-base extension of the oligos on the BeadChip, using the captured DNA as a template, incorporates tagged nucleotides on the BeadChip, which are subsequently fluorophore-labeled during staining. The fluorescent label determines the genotype call for the sample.

scan_protocol: The Illumina iScan scans the BeadChips at two wavelengths to detect the fluorescent label, creating image files that are converted into genotype calls based on the detected fluorescence.

data_processing: Genomic DNA extracted from primary melanocytes was genotyped using Illumina Infinium human OmniExpress array

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: primary melanocyte

label_protocol: 200ng of genomic DNA, quantitated using Quant-iT™ PicoGreen dsDNA Reagent (ThermoFisher Scientific, Waltham, MA, USA) is denatured and neutralized, then isothermally amplified by whole-genome amplification.  The amplified product is enzymatically fragmented, then precipitated and re-suspended.

growth_protocol: Primary melanocyte cultures were grown in Dermal Cell Basal Medium (ATCC® PCS-200-030™) supplemented with Melanocyte Growth Kit (ATCC® PCS-200-041™) and 1% Amphotericin B/Penicillin/Streptomycin (120-096-711, Quality Biological) at 37°C with 5% CO2, and trypsinized with Trypsin/EDTA Solution (R-001-100, Cascade Biologics) as well as Trypsin Neutralizer Solution (R-002-100, Cascade Biologics). Media was changed every 2-3 days when necessary.

extract_protocol: Genomic DNA was isolated from primary melanocyte cultrue using Gentra Puregene Cell Kit (158745, Qiagen)

tag: disease

value: Melanocyte

value: SKin


title: Patient_300

value: Regorafenib 160 mg

value: FALSE


title: primary melanocyte C178_2


title: primary melanocyte C26_3


title: primary melanocyte C252_2


title: primary melanocyte C326_2


title: Patient_299


title: Patient_298


title: primary melanocyte C25_2


title: Patient_297


title: primary melanocyte C291_2


title: Patient_296


title: primary melanocyte C304_2


title: Patient_295


title: primary melanocyte C83_2


title: primary melanocyte C91_2


title: primary melanocyte C26_2


title: primary melanocyte C327_2


title: primary melanocyte C291_1


title: Patient_292


title: Patient_293


title: primary melanocyte C201_2


title: Patient_291


title: primary melanocyte C252_1


title: primary melanocyte C91_1


title: primary melanocyte C140_1


title: Patient_294


title: Patient_288


title: primary melanocyte C326_1


title: primary melanocyte C185_1


title: primary melanocyte C304_1


title: primary melanocyte C24_1


title: Patient_290


title: Patient_287


title: Patient_286


title: Patient_285


title: primary melanocyte C25_1


title: primary melanocyte C146_1


title: Patient_284


title: Patient_283


title: Native80_YPD_rep1_R9

first: Carl

middle: G

last: de Boer

address: 415 Main St

institute: The Broad Institute

library_source: genomic

data_processing:
The paired reads representing both sides of the promoter sequence were aligned using the overlapping sequence in the middle, constrained to have 40 (+/-15) bp of overlap, and discarding any reads that failed to align well within these constraints. The scaffold library instead used 16)+/-10) bp of overlap. This was not required for the Native80 library
Promoters were aligned to themselves using Bowtie2 to identify clusters of related sequences, merging these clusters and taking the sequence with the most reads as the “true” promoter sequence for each cluster. The scaffold library was aligned to the designed scaffold sequences, yielding a cluster of sequences derived from each scaffold, which were then subclustered based on the random 80-mer contained within using CD-HIT.  The Native80 library was aligned to the promoter sequences we ordered using Bowtie2.
Mean expression level for each promoter (as in the processed files) was taken as the average of the bins, weighted by the number of times the promoter was observed in each bin. Here, bin labels are in the reverse order of expression (i.e. they reflect RFP/YFP).  Note that Abf1TATA sorting bin 16 (R4) was accidentally pooled with part of bin 11 (R9) and so was left out of all analyses and the processed data.
Genome_build: R64
Supplementary_files_format_and_content: compressed text files containing promoter sequences and their corresponding expression levels

organism: Saccharomyces cerevisiae

source_name: Promoter library

growth_protocol: Libraries were transformed into yeast (strain S288C deltaUra3 for Native80 and Y8205 for the others) using the lithium acetate method, starting with 1L of yeast harvested at an OD of 0.3-0.4 , ensuring a complexity of at least 1E8 was achieved for random libraries (with the exception of the high-quality pTpA library where a dilution series was performed to achieve the desired complexity). The yeast were then grown in SD-Ura for two days, diluting the media by 1:4 three times during this period.  Media was then changed to YPD, growing for at least 5 generations prior to cell sorting. For YPGly and YPGal experiments, the same pTpA transformation was used and the culture was grown for at least 8 generations (due to the change in carbon source). In the final 10 hours of growth prior to cell sorting, the cultures were allowed to grow continuously in log phase, never achieving an OD above 0.6, by diluting in fresh media.  All cultures were grown in a shaker incubator, at 30C and approximately 250 RPM.

extract_protocol:
Cells were sorted by the log ratio of RFP to YFP signal (using mCherry and GFP absorption/emission) on a Beckman-Coulter MoFlo Astrios, using 18 uniform bins (except for scaffold library, where bins were approximarely proportional to the expression variance within the bin), done in three batches of six bins each. We note that the FACS configuration varied between experiments (e.g. different laser intensities), resulting in different baseline expression values. Post sort, cells were spun down and resuspended in SC-Ura (supplemented with 1% Gal for Gal sort) and grown for 2-3 days, shaking at 30C.
The plasmids were then isolated, the promoter region amplified, Nextera adaptors and multiplexing indices added, and the resulting libraries sequenced paired-end, 76 bp each, using 150 cycle kits so that complete coverage of the promoter could be achieved, including overlap in the center. The scaffold library was sequenced with 300 cycle kits in two reads of 190 and 110 bases. The second replicate of the Native80 library was sequenced with a 300 cycle kit.

treatment_protocol: Prior to sort, yeast were spun down, washed once in ice-cold PBS, and then suspended in ice-cold PBS and kept on ice until cell sorting.

tag: media

value: YPD

tag: libraryid


title: Patient_282

source_name: plasma

tag: arm

value: good


title: Native80_YPD_rep1_R8


title: primary melanocyte C336_1


title: primary melanocyte C12_1


title: primary melanocyte C83_1


title: Native80_YPD_rep1_R7


title: primary melanocyte C178_1


title: DU145 PAGE4

city: Shenyang

first: Chengcheng

last: Lv

state: Liaoning

address: 44. Xiaoheyan Road

department: Department of Urology Surgery

institute: Liaoning Cancer Hospital and Institute

description:
DU145_gene_count_matrix
DU145.PAGE4.Vehicle

data_processing:
base calling（Illumina 1.8+ Phred+33, raw reads typically (2, 40)）
Raw RNA sequences data were then mapped to the GRCh38 (hg38) genome using HISAT2 2.1.0
FeatureCounts 1.6.0 was used to count reads and generate raw counts for per gene
Genome_build: GRCh38
Supplementary_files_format_and_content: gene counts in csv

source_name: DU145 cell line

growth_protocol: All cells were cultured in 1640 containing 10% fetal bovine serum.

extract_protocol:
one million cells each were collected , and RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 200mM hydrogen peroxide which was used to stimulate ROS and PBS which was used as control were added to cells 12 hours before collection.

tag: cell line

value: DU145 cell line

tag: protocol


title: primary melanocyte C230_1


title: Patient_280

tag: os

tag: ttp

tag: batch


title: Native80_YPD_rep1_R6


title: primary melanocyte C251_1


title: Patient_289

tag: unisp2 outlier

tag: unisp4 outlier

tag: unisp6 outlier


title: Patient_281

tag: cel-mir-39-3p outlier

tag: dct hemo

tag: hemo status

value: bad


title: DU145 Vector H2O2

description:
DU145_gene_count_matrix
DU145.TET.H2O2

value: Vector H2O2


title: Native80_YPD_rep1_R5

tag: strain


title: DU145 Vector

description:
DU145_gene_count_matrix
DU145.TET.Vehicle

value: Vector


title: Patient_278


title: Patient_279


title: primary melanocyte C290_1

tag: tissue


title: Native80_YPD_rep1_R4


title: primary melanocyte C173_1

tag: disease


title: Patient_277


title: primary melanocyte C18_1


title: Native80_YPD_rep1_R3

tag: media


title: 22RV1 PAGE4

description:
22RV1_gene_count_matrix
x22RV1.PAGE4.Vehicle

source_name: 22RV1 cell line

value: 22RV1 cell line


title: Native80_YPD_rep1_R2

tag: libraryid


title: primary melanocyte C200_1


title: 22RV1 Vector H2O2

description:
22RV1_gene_count_matrix
x22RV1.TET.H2O2


title: Patient_276

tag: arm

value: Placebo


title: primary melanocyte C24_2


title: Patient_275


title: primary melanocyte C360_1


title: 22RV1 PAGE4 H2O2

description:
22RV1_gene_count_matrix
x22RV1.PAGE4.H2O2

tag: cell line

value: PAGE4 H2O2


title: primary melanocyte C31_1


title: Native80_YPD_rep1_R19


title: 22RV1 Vector

description:
22RV1_gene_count_matrix
x22RV1.TET.Vehicle

tag: protocol


title: Native80_YPD_rep1_R18


title: Patient_274

tag: os


title: DU145 PAGE4 H2O2

description:
DU145_gene_count_matrix
DU145.PAGE4.H2O2


title: S912: DARP-EGFP line 2, SUPT4H1 siRNAs, replicate 2

data_processing:
Sequencing adapters were trimmed using skewer (Jiang et al., 2014; version 0.2.2) with default parameters. Quality control of the trimmed reads was performed using FastQC (version 0.11.5: www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were aligned to a composite index of the human genome (version GRCh38_p10) and sequences of the 92 ERCC spike-in transcripts: A STAR index (Dobin et al., 2013; version 2.5.3a) was built with the --sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release 27) were provided via the --sjdbGTFfile argument. STAR alignments were generated with the following parameters: --outFilterType BySJout --quantMode TranscriptomeSAM --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM MD XS --outSAMunmapped Within
Transcript abundance was quantified based on the STAR alignments using salmon (Patro et al., 2017; version 0.9.1) with the following parameters: --seqBias --gcBias --biasSpeedSamp 10 with Gencode gene models (version 27). Post-alignment quality control reports were generated using MultiQC (Ewels et al., 2016; version 1.0).
Transcript abundances were imported with the tximport Bioconductor package (Soneson et al., 2015; version 1.6.0) and aggregated to gene level counts using the "scaledTPM" option using R (version 3.4.3). Gene symbols and Entrez gene identifiers were mapped using Ensembl (version 86) via the biomaRt R package (Durinck et al, 2009; version 2.34.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited, gzip-compressed text file with matrix of raw quantitation results for each sample.

source_name: Human embryonic kidney

extract_protocol:
72 hours post transfection, total RNA was extracted with the RNEasy (Qiagen) kit from 750,000 cells per sample.  Either ERCC mix1 or mix2 external standards (Invitrogen) were diluted 1:100 in water and 1 ul was added to each lysate.
Sequencing libraries were generated by SeqMatic (Fremont, CA). rRNA was depleted with the Ribo-Zero Gold rRNA Removal Kit (Illumina) and sequencing libraries were prepared with the TruSeq Stranded Total RNA kit (Illumina).

value: Human embryonic kidney

tag: exogenous gene expressed

value: DARP-EGFP

tag: treatment

value: SUPT4H1 siRNAs

tag: ercc mix

tag: hours post-infection

value: 72 hours

tag: rin

tag: replicate


title: primary melanocyte C7_1

value: Melanocyte


title: primary melanocyte C77_1

value: SKin


title: primary melanocyte C192_1


title: Patient_273

tag: ttp

tag: batch

tag: unisp2 outlier

tag: unisp4 outlier

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo


title: S832: DARP-EGFP line 2, SUPT4H1 siRNAs, replicate 1

tag: tissue


title: Native80_YPD_rep1_R16

tag: media

tag: libraryid

tag: strain


title: Patient_272

tag: arm

value: Regorafenib 160 mg

tag: os

tag: hemo status


title: S783: DARP-EGFP line 1, scrambled siRNAs, replicate 2

tag: cell line

tag: exogenous gene expressed

tag: treatment

value: scrambled siRNAs

tag: ercc mix

tag: hours post-infection


title: Native80_YPD_rep1_R15

value: YPD


title: primary melanocyte C239_1

tag: disease


title: Patient_271

tag: ttp

tag: batch

tag: unisp2 outlier

value: FALSE

tag: unisp4 outlier

value: good


title: Native80_YPD_rep1_R14


title: primary melanocyte C165_1

tag: tissue


title: S622: DARP-EGFP line 2, scrambled siRNAs, replicate 2

tag: rin

tag: replicate


title: Native80_YPD_rep1_R13

tag: media

tag: libraryid

tag: strain


title: Native80_YPD_rep1_R17


title: Patient_269

tag: arm

tag: os

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo

tag: hemo status


title: primary melanocyte C204_1

tag: disease


title: primary melanocyte C78_1


title: Patient_268

tag: ttp


title: Patient_270

tag: batch


title: Native80_YPD_rep1_R12


title: Native80_YPD_rep1_R11


title: Patient_267

tag: unisp2 outlier


title: Native80_YPD_rep1_R10


title: Patient_266

tag: unisp4 outlier


title: primary melanocyte C26_1

tag: tissue


title: S420: EGFP line, SUPT4H1 siRNAs, replicate 1

tag: cell line

tag: exogenous gene expressed

value: EGFP

tag: treatment

tag: ercc mix

tag: hours post-infection

tag: rin


title: primary melanocyte C64_1


title: S320: DARP-EGFP line 1, scrambled siRNAs, replicate 1

tag: replicate


title: Native80_YPD_rep2_R9

tag: media

tag: libraryid

tag: strain


title: S458: EGFP line, scrambled siRNAs, replicate 2


title: S487: DARP-EGFP line 1, SUPT4H1 siRNAs, replicate 2


title: primary melanocyte C34_1


title: S255: EGFP line, scrambled siRNAs, replicate 1


title: Patient_264

tag: arm

tag: os

tag: unisp6 outlier

tag: cel-mir-39-3p outlier

tag: dct hemo

tag: hemo status


title: S190: DARP-EGFP line 1, SUPT4H1 siRNAs, replicate 1

tag: tissue


title: Native80_YPD_rep2_R7


title: Native80_YPD_rep2_R8


title: primary melanocyte C87_1

tag: disease


title: S623: EGFP line, SUPT4H1 siRNAs, replicate 2

tag: cell line

tag: exogenous gene expressed


title: S168: DARP-EGFP line 2, scrambled siRNAs, replicate 1

tag: treatment

tag: ercc mix


title: Native80_YPD_rep2_R6


title: Patient_265

tag: ttp

tag: batch

tag: unisp2 outlier

tag: unisp4 outlier


title: Arsenopyrite (FeAsS) exposure treatment (T_2)

city: Tainan

first: Jiin-Shuh

last: Jean

address: 1st University Road

department: Department of Earth Science

country: Taiwan

institute: National Cheng Kung University

data_processing:
Illumina official tool, BCL2FASTQ conversion Software v2.20 was used to convert BCL files from the Illumina NextSeq500 sequencing platform.
TRIMMOMATIC v0.32 was used to remove adaptors and trim low quality bases.
Trimmed reads were aligned to the reference genome sequence using HISAT2 v2.1.0 aligner to produce SAM file and then converted to sorted BAM files using SAMTOOLS v1.2.
Differential expression analysis was performed using CUFFDIFF of CUFFLINKS package v2.2.1 to produce count and FPKM profiles for each group of samples.
Genome_build: Lysinibacillus sp. B2A1 (CP027224)
Supplementary_files_format_and_content: excel file include FPKM values for each group of samples

organism: Lysinibacillus sp. B2A1

source_name: Bacteria

growth_protocol: Bacterial cells grown in chemical defined medium up to log phase.

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual. 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 labchip kit (Agilent Technologies, USA).
All RNA Sample preparation procedures were carried out according to the official Illumina protocol. Agilent's SureSelect Strand Specific RNA Library Preparation Kit was used for library construction followed by AMPure XP Beads size selection.

treatment_protocol: Log phase bacterial cells collected and washed three times with PBS and incubated with arsenopyrite (FeAsS) and no arsenic mineral (control) under the artificial groundwater medium for 12 h. (Experiment was done in biological duplicate)

value: whole organism


title: Patient_261

value: medium


title: Arsenopyrite (FeAsS) exposure treatment (T_1)


title: Patient_262


title: Patient_260


title: Patient_263


title: Native80_YPD_rep2_R5

tag: media

tag: libraryid

tag: strain


title: primary melanocyte C245_1


title: primary melanocyte C174_1


title: primary melanocyte C76_1


title: primary melanocyte C167_1


title: Native80_YPD_rep2_R4


title: primary melanocyte C22_1


title: No As-mineral exposure control (C_2)


title: Patient_259

tag: arm

tag: os

tag: unisp6 outlier


title: No As-mineral exposure control (C_1)


title: primary melanocyte C80_1


title: Native80_YPD_rep2_R2


title: Native80_YPD_rep2_R3


title: primary melanocyte C168_1


title: Patient_257

tag: cel-mir-39-3p outlier

tag: dct hemo

tag: hemo status


title: Native80_YPD_rep2_R19


title: dcreA_cellulose_rep3

city: Qingdao

first: Guodong

last: Liu

state: Shandong

address: Binhai Road 72

department: State Key Laboratory of Microbial Technology

institute: Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, and were trimmed for the bases from both the 3' end and 5' end when the base quality is below 3. We also slides a 4-base window from the 5' end and cuts reads when the mean quality falls below 18. Then, the reads that are shorter than 36 bp after trimming were filtered out.
Sequenced reads were aligned to the genome using hisat2 2.0.0-beta with default parameters for paired-end reads.
Raw counts of mapped reads on gene-level were quantificated using featureCounts v1.5.0-p1 with "-s 2" parameter specified for "reverse" stranded-specific library construction.
The measure FPKM (fragments per kilobase per million mapped fragments) was used to show the gene expression values. Deseq2 normailization was used latter to compare the gene expression levels between samples and perform statistical analysis.
Genome_build: Penicillium oxalicum 114-2 genomic sequence (NCBI accession: PRJNA60877)
Supplementary_files_format_and_content: One matrix table in text format including FPKM values for each genes.

organism: Penicillium oxalicum

source_name: Fungal mycelia

growth_protocol: All strains were first precultured in Vogel's medium with 2% glucose for 22 h, and then transferred to Vogel's medium with indicated carbon sources for 4 hours cultivation at 30 degrees C, 200 rpm.

extract_protocol:
Total RNA was prepared from the mycelia by grinding under liquid nitrogen with a mortar and pestle, followed by extraction using the RNAisoTM reagent (TaKaRa, Japan) according to manufacturer's protocol.
mRNA libraries were prepared for sequencing using KAPA mRNA Capture Kit and KAPA Stranded RNA-Seq Kit according to the manufacturer's instructions.

treatment_protocol: Mycelia were filtered by filter paper.

value: creA deletion mutant deltacreA

tag: tissue

value: Fungal mycelia

tag: carbon source

value: 2% (w/v) cellulose


title: dcreA_cellulose_rep2


title: Patient_258


title: dcreA_cellulose_rep1


title: Native80_YPD_rep2_R18


title: Patient_256


title: Patient_255

value: Placebo


title: Native80_YPD_rep2_R17


title: gClrBID_cellulose_rep3

value: ClrB internal mutant overexpression strain gClrBID


title: Native80_YPD_rep2_R16


title: primary melanocyte C318_1

tag: disease


title: gClrBID_cellulose_rep2


title: primary melanocyte C193_1


title: Native80_YPD_rep2_R15


title: Patient_254


title: Patient_252


title: primary melanocyte C191_1


title: Patient_253


title: gClrBID_cellulose_rep1


title: M12_cellulose_rep3

value: Reference strain M12


title: Native80_YPD_rep2_R14


title: Native80_YPD_rep2_R13


title: primary melanocyte C14_1


title: M12_cellulose_rep2


title: Native80_YPD_rep2_R12


title: primary melanocyte C73_1


title: primary melanocyte C206_1


title: M12_cellulose_rep1


title: Patient_250


title: Native80_YPD_rep2_R11


title: gClrBID_glucose_rep3

value: 2% (w/v) glucose


title: Native80_YPD_rep2_R10


title: Scaffold_1E7_YPD_R19

data_processing:
The paired reads representing both sides of the promoter sequence were aligned using the overlapping sequence in the middle, constrained to have 40 (+/-15) bp of overlap, and discarding any reads that failed to align well within these constraints. The scaffold library instead used 16)+/-10) bp of overlap.
Promoters were aligned to themselves using Bowtie2 to identify clusters of related sequences, merging these clusters and taking the sequence with the most reads as the “true” promoter sequence for each cluster. The scaffold library was aligned to the designed scaffold sequences, yielding a cluster of sequences derived from each scaffold, which were then subclustered based on the random 80-mer contained within using CD-HIT.
Mean expression level for each promoter (as in the processed files) was taken as the average of the bins, weighted by the number of times the promoter was observed in each bin. Here, bin labels are in the reverse order of expression (i.e. they reflect RFP/YFP).  Note that Abf1TATA sorting bin 16 (R4) was accidentally pooled with part of bin 11 (R9) and so was left out of all analyses and the processed data.
Genome_build: R64
Supplementary_files_format_and_content: compressed text files containing promoter sequences and their corresponding expression levels

source_name: Random promoter library

growth_protocol: Libraries were transformed into yeast (strain Y8205) using the lithium acetate method, starting with 1L of yeast harvested at an OD of 0.3-0.4 , ensuring a complexity of at least 1E8 was achieved (with the exception of the high-quality pTpA library where a dilution series was performed to achieve the desired complexity). The yeast were then grown in SD-Ura for two days, diluting the media by 1:4 three times during this period.  Media was then changed to YPD, growing for at least 5 generations prior to cell sorting. For YPGly and YPGal experiments, the same pTpA transformation was used and the culture was grown for at least 8 generations (due to the change in carbon source). In the final 10 hours of growth prior to cell sorting, the cultures were allowed to grow continuously in log phase, never achieving an OD above 0.6, by diluting in fresh media.  All cultures were grown in a shaker incubator, at 30C and approximately 250 RPM.

extract_protocol:
Cells were sorted by the log ratio of RFP to YFP signal (using mCherry and GFP absorption/emission) on a Beckman-Coulter MoFlo Astrios, using 18 uniform bins (except for scaffold library, where bins were approximarely proportional to the expression variance within the bin), done in three batches of six bins each. We note that the FACS configuration varied between experiments (e.g. different laser intensities), resulting in different baseline expression values. Post sort, cells were spun down and resuspended in SC-Ura (supplemented with 1% Gal for Gal sort) and grown for 2-3 days, shaking at 30C.
The plasmids were then isolated, the promoter region amplified, Nextera adaptors and multiplexing indices added, and the resulting libraries sequenced paired-end, 76 bp each, using 150 cycle kits so that complete coverage of the promoter could be achieved, including overlap in the center. The scaffold library was sequenced with 300 cycle kits in two reads of 190 and 110 bases.


title: Patient_247


title: primary melanocyte CSD2_1

value: Melanocyte


title: primary melanocyte C254_1

value: SKin


title: Patient_248

value: Regorafenib 160 mg


title: Patient_251


title: Patient_246


title: gClrBID_glucose_rep1


title: Scaffold_1E7_YPD_R18


title: M12_glucose_rep3


title: Scaffold_1E7_YPD_R17


title: Patient_245


title: primary melanocyte C241_1


title: primary melanocyte C223_1


title: Patient_249


title: M12_glucose_rep2


title: primary melanocyte C28_1


title: primary melanocyte CSD1_1


title: primary melanocyte C20_1


title: Patient_244


title: Scaffold_1E7_YPD_R16


title: Patient_243


title: primary melanocyte C234_1


title: Scaffold_1E7_YPD_R15


title: Scaffold_1E7_YPD_R14


title: primary melanocyte C344_1


title: Patient_241


title: Patient_242


title: Scaffold_1E7_YPD_R13


title: M12_glucose_rep1


title: gClrBID_glucose_rep2


title: Patient_240


title: Patient 45

description: Patient 45

data_processing: Analyzed with NanoString nSolver 3.0 including the nCounter Advanced Analysis module (version 1.1.4) with default parameters

source_name: tumor tissue (FFPE)

extract_protocol: Total RNA was extracted from FFPE tissue after tumor microdissection using the High Pure FFPE RNA isolation kit from Roche


title: Patient 44

description: Patient 44


title: primary melanocyte C198_1


title: primary melanocyte C303_1


title: Scaffold_1E7_YPD_R11


title: primary melanocyte C23_1


title: Patient_239


title: Patient 43

description: Patient 43


title: Patient_238


title: primary melanocyte C130_1


title: primary melanocyte C218_1


title: Patient 42

description: Patient 42


title: Patient_237


title: Scaffold_1E7_YPD_R10


title: Scaffold_1E7_YPD_R9


title: Patient 41

description: Patient 41


title: Patient 46

description: Patient 46


title: Patient_236


title: Scaffold_1E7_YPD_R8


title: Patient_235


title: Scaffold_1E7_YPD_R7


title: Patient 40

description: Patient 40


title: Scaffold_1E7_YPD_R6


title: Scaffold_1E7_YPD_R12


title: Patient 38

description: Patient 38


title: Patient_234


title: Patient_233


title: Patient 37

description: Patient 37


title: Scaffold_1E7_YPD_R5


title: Patient_232


title: primary melanocyte C250_1


title: Patient 36

description: Patient 36


title: Scaffold_1E7_YPD_R4


title: primary melanocyte C54_1


title: primary melanocyte C355_1


title: Patient_231


title: Patient 35

description: Patient 35


title: Scaffold_1E7_YPD_R3


title: primary melanocyte C262_1


title: Patient 34

description: Patient 34


title: Scaffold_1E7_YPD_R2


title: Patient_230


title: primary melanocyte C74_1


title: primary melanocyte C53_1


title: primary melanocyte C21_1


title: Patient_229


title: primary melanocyte C16_1


title: Patient_228


title: Patient 32

description: Patient 32


title: Patient_227


title: Patient 39

description: Patient 39


title: Patient 31

description: Patient 31


title: primary melanocyte C88_1


title: Patient_226


title: Patient 30

description: Patient 30


title: primary melanocyte C15_1


title: primary melanocyte C38_1


title: primary melanocyte C220_1


title: primary melanocyte C240_1


title: Patient 29

description: Patient 29


title: Patient_224


title: Patient_225


title: Patient 27

description: Patient 27


title: Patient_223


title: Patient 28

description: Patient 28


title: primary melanocyte C225_1


title: primary melanocyte C8_1


title: Patient_222


title: Patient 33

description: Patient 33


title: Patient 26

description: Patient 26


title: Patient_221


title: Patient 25

description: Patient 25


title: primary melanocyte C43_1


title: pTpA_1E8_YPGly_R9

description: 20161024_average_promoter_ELs_per_seq_3p1E7_Gly_ALL.shuffled.txt.gz

data_processing:
The paired reads representing both sides of the promoter sequence were aligned using the overlapping sequence in the middle, constrained to have 40 (+/-15) bp of overlap, and discarding any reads that failed to align well within these constraints.
Promoters were aligned to themselves using Bowtie2 (72) to identify clusters of related sequences, merging these clusters and taking the sequence with the most reads as the “true” promoter sequence for each cluster.
Mean expression level for each promoter (as in the processed files) was taken as the average of the bins, weighted by the number of times the promoter was observed in each bin. Here, bin labels are in the reverse order of expression (i.e. they reflect RFP/YFP).  Note that Abf1TATA sorting bin 16 (R4) was accidentally pooled with part of bin 11 (R9) and so was left out of all analyses and the processed data.
Genome_build: R64
Supplementary_files_format_and_content: compressed text files containing promoter sequences and their corresponding expression levels

extract_protocol:
Plasmids were isolated using Qiagen spin miniprep kits, as adapted for yeast according to the manufacturer's website. Cells were sorted by the log ratio of RFP to YFP signal (using mCherry and GFP absorption/emission) on a Beckman-Coulter MoFlo Astrios, using 18 uniform bins, done in three batches of six bins each. We note that the FACS configuration varied between experiments (e.g. different laser intensities), resulting in different baseline expression values. Post sort, cells were spun down and resuspended in SC-Ura (supplemented with 1% Gal for Gal sort) and grown for 2-3 days, shaking at 30C.
The plasmids were then isolated, the promoter region amplified, Nextera adaptors and multiplexing indices added, and the resulting libraries sequenced paired-end, 76 bp each, using 150 cycle kits so that complete coverage of the promoter could be achieved, including overlap in the center.

value: YPGly


title: pTpA_1E8_YPGly_R8


title: Patient 24

description: Patient 24


title: Patient_220


title: Patient_219


title: pTpA_1E8_YPGly_R7


title: Patient 23

description: Patient 23


title: primary melanocyte C166_1


title: pTpA_1E8_YPGly_R6


title: Patient 22

description: Patient 22


title: pTpA_1E8_YPGly_R5


title: Patient 21

description: Patient 21


title: primary melanocyte C71_1


title: Patient_217


title: primary melanocyte C238_1


title: primary melanocyte C17_1


title: Patient_218


title: Patient_216


title: pTpA_1E8_YPGly_R4


title: Patient 20

description: Patient 20


title: pTpA_1E8_YPGly_R3


title: Patient_215


title: Patient 18

description: Patient 18


title: primary melanocyte C65_1


title: Patient_214


title: pTpA_1E8_YPGly_R2


title: Patient 17

description: Patient 17


title: Patient_213


title: primary melanocyte C134_1


title: Patient 19

description: Patient 19


title: pTpA_1E8_YPGly_R19


title: Patient_212


title: Patient 16

description: Patient 16


title: Patient 15

description: Patient 15


title: Patient_211


title: primary melanocyte C68_1


title: pTpA_1E8_YPGly_R16


title: pTpA_1E8_YPGly_R18


title: pTpA_1E8_YPGly_R17


title: Patient_209


title: Patient 14

description: Patient 14


title: Patient 13

description: Patient 13


title: pTpA_1E8_YPGly_R15


title: Patient_210


title: primary melanocyte C282_1


title: Patient_208


title: pTpA_1E8_YPGly_R14


title: Patient 12

description: Patient 12


title: primary melanocyte C283_1


title: primary melanocyte C363_1


title: Patient 11

description: Patient 11


title: pTpA_1E8_YPGly_R13


title: Patient_207


title: pTpA_1E8_YPGly_R12


title: Patient 10

description: Patient 10


title: primary melanocyte C179_1


title: primary melanocyte C6_1


title: primary melanocyte C197_1


title: primary melanocyte C365_1


title: Patient_205


title: primary melanocyte C219_1


title: Patient 9

description: Patient 9


title: primary melanocyte C327_1


title: primary melanocyte C27_1


title: primary melanocyte C62_1


title: Patient_204


title: Patient 8

description: Patient 8


title: pTpA_1E8_YPGly_R10


title: 10: NAC NSC

city: New york

first: Jihye

last: Paik

address: 1300 York Ave.

department: Pathology

data_processing:
Basecalls performed using BaseCall  version 1.1.2
Sequenced reads with adaptor sequence or low-quality sequence (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 20% in a read) are discarded and then mapped to mm10 whole genome using HISAT2 v2.0.4 with parameters:  --phred64 --sensitive --no-discordant --no-mixed -I  1 -X 1000, mapped to gene reference using Bowtie2 v2.2.5 with parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200 and then calculate gene expression level with RSEM. RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
Screening DEGs using EBSeq,we defined a gene as a DEG (differentially expressed gene) when foldchange ≥2 and PPEE ≤ 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited txt files include FPKM values for each Sample.

source_name: Neural progenitor cells

growth_protocol: N2 media with EGF and bFGF

extract_protocol:
TRIZOL
1) Total RNA treatment  a) RNase H Probe (rRNA depletion): Hybridize the rRNA with DNA probe and digest the DNA/RNA  hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after  purification.  b) Oligo dT Selection (mRNA enrichment): Use oligo dT beads to select mRNA with poly A tail.  2) RNA fragment and reverse transcription  Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer.  3) End repair and adaptor ligation  End repair the dscDNA to blunt end and phosphate at 5’ end, 3’ end forms an “A” cohesive end. And  then ligate to the bubble adapter with protruding T of 3’ end.  4) PCR amplification  5) Single strand separation and cyclization  Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA  ligase.  6)DNA nanoball making7) Sequencing on BGISEQ-500 platform

treatment_protocol: 48 hrs with PQ or NAC

value: Neural progenitor cells


title: 12: PQ NSC


title: pTpA_1E8_YPGal_R9

city: Cambridge

description: 20161024_average_promoter_ELs_per_seq_3p1E7_Gal_ALL.shuffled.txt.gz

value: YPGal


title: Patient_206

value: FALSE


title: Patient 7

description: Patient 7


title: Patient_203

value: good


title: primary melanocyte C29_1


title: pTpA_1E8_YPGal_R8


title: Patient 6

description: Patient 6


title: pTpA_1E8_YPGly_R11


title: Patient_202


title: 9: PQ NSC


title: Patient 5

description: Patient 5


title: 11: control NSC


title: primary melanocyte C194_1


title: pTpA_1E8_YPGal_R6


title: Patient_200


title: pTpA_1E8_YPGal_R7


title: 8: control NSC


title: primary melanocyte C195_1


title: 1: input

data_processing:
Basecalls performed using BaseCall version 1.1.2
ChIP-seq reads were aligned to the mm10 genome assembly using SOAPaligner/soap2 version 2.21 with the following configurations：-v 2 -s 35 -m 50 -x 600
Data were filtered using the following specifications：Sequenced reads with adaptor sequence or low-quality sequence (we define the low quality read as the percentage of base which quality is lesser than 5 is greater than 50% in a read) are discarded
Peaks were called using macs2 version 2.1.0 with the following setting: --bw 200 -g mm -s 49 -p 1e-5 -m 10 30
Genome_build: mm10
Supplementary_files_format_and_content: Bw files were transformed from wig files generated using macs2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
a) End repair, Adaptor ligation: The ends of the IP / Input DNA are complemented and phosphorylated at the 5 'end, the 3' end is protruded a
sticky end of "A" and then a bubbly joint with a "T" protruding at the 3 'end.
b) PCR amplification: The ligation product is subjected to PCR amplification by specific primers.
c) Single chain separation and cyclization: PCR products are heat-denatured into single-stranded, and then single-stranded DNA is cyclized with a bridge
primer to obtain a single-stranded circular DNA library.
d) Sequencing: Sequencing is performed using the resulting amplified product DNA Nano balls (DNB).

value: adult neural progenitor cells


title: Patient 4

description: Patient 4


title: Patient_199


title: primary melanocyte C55_1


title: Patient 3

description: Patient 3


title: primary melanocyte C160_1


title: pTpA_1E8_YPGal_R4


title: primary melanocyte C205_1


title: primary melanocyte C244_1


title: Patient_198


title: pTpA_1E8_YPGal_R5


title: pTpA_1E8_YPGal_R3


title: Patient_197


title: Patient 1

description: Patient 1


title: Patient 2

description: Patient 2