title: YKL023W_YKL023W_DEL_2

description: Comparison of double mutant abundance in populations containing the deletion of a target gene compared with a reference population

hyb_protocol: 8. Add 50 µl DIG Easy Hyb buffer to the pellet. Mix by repeated pipetting. Dilute 20 µl of the sample with 100 µl DIG Easy Hyb and keep the rest at -20°C, for the case when the hybridization needs to be repeated. Heat for 2 minutes at 95°C and then switch to ice for 5 minutes. Keep the sample at room temperature until hybridization.9. Add the cover slide, with the gaskets, to the lower part of the hybridization chamber. Pipet carefully 47 µl of sample in the middle of a gasket square. Carefully layer the microarray slide over the sample, oligonucleotide side down (can be detected by breathing on the sides of the slide) and close the hybridizaton chamber. Pay attention that a single air bubble is formed in the chamber. Place the chamber on a rotating wheel (see Note 12.) in a 24 °C incubator for at least 12 hours.10. Prepare several dilutions of SSPE buffer (6x, 2x, 0.2x) containing 0.05% Triton X100. Pre-heat 50 ml SSPE 6X, 0.05% Triton X100 at 30°C. Open the chamber and transfer the two slides together in a Falcon tube with the wash 6X SSPE buffer. Remove the slide with the gaskets and transfer the microarray slide to a second bath of 6x SSPE, 0.05% Triton X100. Leave for 5 minutes with occasional agitation, then move the slide to the 2X SSPE solution, 0.2X SSPE solution and finally to a 0.2X SSPE solution containing no Triton X100. Incubate at each step for 5 minutes (RT). 11. After the last wash, slowly remove the slide from the liquid, dry its lower edge on a piece of Whatman paper, and plunge in stabilization solution for 10 seconds (under a chemical hood). Slowly remove the slide from the liquid so that no droplets remain; droplets can also be removed by a flux of dry air.

source_name: S. cerevisiae GIM pool

label_protocol: 4. Use 1 μl of the previously prepared DNA extract as template in each of two PCR reactions that are set up using oligonucleotides U1-KU (uptag PCR 1, UPCR1) and D1-KD (downtag PCR 1, DPCR1) (see Fig. 1a and Note 9.). Set up standard 50 µl reactions for each PCR reaction (25 cycles, 94°C denaturation 30 sec., 50°C annealing 30 sec., 72°C elongation 30 sec). Verify the size and abundance of PCR products by electrophoresis on a 1% agarose gel.5. Prepare four different PCR reactions for each comparison between a screen using a query mutation and a screen performed under identical conditions with a reference mutation. Set up standard 50 µl PCR reaction with 0.5 µl UPCR1 or DPCR1 in the following combinations with oligonucleotides: UPCR1 query with oligonucleotides U1 and U2-Cy3, UPCR1 reference with oligonucleotides U1 and U2-Cy5, DPCR1 query with oligonucleotides D1 and D2-Cy3, DPCR1 reference with oligonucleotides D1 and D2-Cy5. Use 15 cycles of amplification (94°C 15 sec, 55°C 15 sec, 72°C 15 sec). Test the reactions by electrophoresis using a 3% agarose gel and a loading buffer that only contains xylene cyanol. The expected size of PCR products is 60 nt.6. Mix the four PCR products obtained in the previous step. Add a pre-mix containing 5µl each of oligonucleotides U1, D1, U2block and D2block (100 µM each, see Note 11.) and 2 µl linear poly-acrylamide (5 mg/ml), as carrier. Add 22.5 µl sodium acetate (3M, pH=5.2), mix well and precipitate with 550 µl pure ethanol. Leave at -20°C for at least one hour.7. Centrifuge 30 minutes at 15 000 g, 4°C. Pay attention to the purple pellet when removing the supernatant. From now on, avoid direct exposure of the pellet or solution to light. Wash the pellet once with 70% ethanol. Recentrifuge 5 minutes at 15 000 g, 4°C. Remove the ethanol and leave the tube on the bench for 5 minutes to dry.

growth_protocol: After selection of double mutant haploid cells, the pool of haploid strains was growth for 18 generations under double antibiotic selection (G418 and nurseothricin).

extract_protocol: 1. Resuspend the cell pellet recovered in the previous step in 0.2 ml extraction buffer (2% Triton X100, 1% SDS, 0.1M NaCl, 10 mM Tris-Hcl pH 8, 1 mm EDTA) and add approximately 0.2 ml acid-washed glass beads (0.4-0.6 mm diameter, Sigma) and 0.2 ml phenol-chloroform-isoamyl alcohol mix (25:24:1, pH 8). Vortex vigorously for 7 minutes under a chemical hood.2. Add 0.2 ml TE buffer and vortex for 5 seconds. Centrifuge at 13 000 g for 10 minutes, at RT. Transfer the supernatant in a 1.5 ml Eppendorf tube that already contains 1 ml pure ethanol. Mix by turning the tube upside down several times. 3. Centrifuge at 13 000 g, at RT, for 5 minutes. Wash the white small pellet that sticks to the bottom of the tube with 0.5 ml of 70% ethanol. Centrifuge at 13 000 g for 5 minutes at RT. Throw the supernatant, leave the pellet at room temperature to dry out, between 5 and 10 minutes and resuspend the dry pellet in 30 μl of TE (optionally add 10 ng/ml RNase A).

treatment_protocol: Recover the equivalent of 10 OD600nm culture for each screen and the corresponding reference pool of cells. Pellet the cells by centrifugation at 3200 g, 10 min, RT, and resuspend in 1 ml ice cold H20, then split in two aliquots in 1.5 ml Eppendorf tubes. Pellet the cells by 20 seconds of 13 000 g centrifugation at 4°C, remove supernatant and freeze the cells at -80°C until further processing.

value: Mix of haploid strains derived from BY4742/BY4741

value: YKL023W deletion pool

tag: date

tag: screen id

source_name: S. cerevisiae reference GIM pool of screens

value: multiple deletion reference mix


title: WholeBlood_CRC305DGENT0203018_Day3

status: Public on Dec 31 2019

type: RNA

city: London

first: David

last: Lewis

address: Du Cane Road

department: ICRF

country: United Kingdom

institute: Imperial College London

description: Whole blood gene expression of participant on day

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented and hybridized to custom whole genome human 8 × 60K multipack microarrays (Agilent-048908) following the manufacturers instructions. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) according the manufacturers protocol.

scan_protocol: Slides were scanned immediately after washing using a high resolution DNA Microarray Scanner (G2505B, Agilent Technologies) with 3 µm resoltion and 20 bit image depth

data_processing: The scanned microarray images were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Blood, PaxGene

label_protocol: Total RNA was amplified and labeled with the low input Quick-Amp Labelling Kit (Agilent Technologies) with cyanine 3-CTP followed by precipitation, purification, and quantification.

extract_protocol: mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer

treatment_protocol: Microarray experiments were performed as single-color hybridization. Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

tag: participant

tag: gender

value: female

tag: age

tag: race

value: white

tag: ethnicity

value: not american hispanic or latino

tag: protocol

tag: treatment

value: FLUADD

tag: day

tag: tissue

value: whole blood


title: WholeBlood_CRC305DGENT1531041_Day3

value: male


title: YLR177W_YLR177W_DEL_2

type: genomic

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

scan_protocol: Genepix 4200AL and GenePix Pro v7

data_processing: The scans were processed using GenePix Pro, v7. The values from the obtained gpr files were filtered to keep only values for spots with an SNR > 10. Next, we performed a loess normalization on groups of probes (UP/DAMP, UP/DELETION, DOWN/DAMP, DOWN/DELETION), followed by aggregation of values for each mutant and a second loess normalization on the aggregated data.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

tag: strain

tag: genotype

value: YLR177W deletion pool


title: WholeBlood_CRC305DGENT1233028_Day7


title: WholeBlood_CRC305DGENT1551038_Day21


title: WholeBlood_CRC305DGENT0421004_Day0


title: YKL023W_YKL023W_DEL_1


title: WholeBlood_CRC305DGENT0393007_Day21


title: YJR084W_YJR084W_DEL_2

value: YJR084W deletion pool


title: WholeBlood_CRC305DGENT0063016_Day3


title: YIL096C_YIL096C_DEL_1

value: YIL096C deletion pool


title: YER010C_YER010C_DEL_2

value: YER010C deletion pool


title: YHR029C_YHI9_DEL_1

value: YHR029C deletion pool


title: YER010C_YER010C_DEL_1

source_name: S. cerevisiae reference GIM screen

value: YEL068C deletion reference mix


title: YHR029C_YHI9_DEL_2


title: WholeBlood_CRC305DGENT1611036_Day0


title: WholeBlood_CRC305DGENT1521035_Day7


title: YCR016W_YCR016W_DEL_1

value: YCR016W deletion pool


title: WholeBlood_CRC305DGENT1423030_Day7


title: YCL001W-A_YCL001W-A_DEL_2

value: YCL001W-A deletion pool


title: YJR084W_YJR084W_DEL_1

value: Mix of haploid strains derived from BY4742/BY4741


title: YBL028C_YBL028C_DEL_2

value: YBL028C deletion pool


title: YCL001W-A_YCL001W-A_DEL_1

value: multiple deletion reference mix


title: WholeBlood_CRC305DGENT1483036_Day1

value: female


title: WholeBlood_CRC305DGENT1631034_Day21

value: white


title: YJL141C_YAK1_DEL_2

value: YJL141C deletion pool


title: WholeBlood_CRC305DGENT0111015_Day7

value: not american hispanic or latino

value: FLUADD


title: YDR049W_VMS1_DEL_4

value: YDR049W deletion pool


title: WholeBlood_CRC305DGENT1291026_Day3

value: male

value: whole blood


title: YDR049W_VMS1_DEL_3


title: WholeBlood_CRC305DGENT0051016_Day7


title: WholeBlood_CRC305DGENT1503022_Day1


title: WholeBlood_CRC305DGENT1573034_Day21


title: YDR049W_VMS1_DEL_1


title: WholeBlood_CRC305DGENT1341027_Day7


title: YDR049W_VMS1_DEL_2


title: WholeBlood_CRC305DGENT1253029_Day0


title: YJL141C_YAK1_DEL_1


title: YGR184C_UBR1_DEL_1

value: YGR184C deletion pool


title: YGR184C_UBR1_DEL_2


title: WholeBlood_CRC305DGENT0393007_Day3


title: YBL028C_YBL028C_DEL_1


title: YMR223W_UBP8_DEL_2

value: YMR223W deletion pool


title: WholeBlood_CRC305DGENT1541033_Day21


title: WholeBlood_CRC305DGENT1581031_Day21


title: WholeBlood_CRC305DGENT1393025_Day0

value: PLACEBOD


title: YMR223W_UBP8_DEL_1


title: WholeBlood_CRC305DGENT2453055_Day7


title: YFR010W_UBP6_DEL_2

value: YFR010W deletion pool


title: WholeBlood_CRC305DGENT2291044_Day1


title: WholeBlood_CRC305DGENT2193048_Day21


title: WholeBlood_CRC305DGENT0241003_Day1


title: YLR177W_YLR177W_DEL_1

value: YLR177W deletion pool


title: WholeBlood_CRC305DGENT2241042_Day3


title: WholeBlood_CRC305DGENT1361021_Day7


title: YOR339C_UBC11_DEL_1

value: YOR339C deletion pool


title: YFR010W_UBP6_DEL_1

value: Mix of haploid strains derived from BY4742/BY4741


title: YDR059C_UBC5_DEL_2

value: YDR059C deletion pool


title: WholeBlood_CRC305DGENT1433024_Day7


title: WholeBlood_CRC305DGENT1341027_Day21


title: WholeBlood_CRC305DGENT2241042_Day21


title: YML014W_TRM9_DEL_1

value: YML014W deletion pool

value: YEL068C deletion reference mix


title: YML014W_TRM9_DEL_2

value: multiple deletion reference mix


title: YNR046W_TRM112_DAMP_3

value: YNR046W DAMP pool


title: YOR339C_UBC11_DEL_2


title: YNR046W_TRM112_DAMP_1


title: YDR059C_UBC5_DEL_1


title: YNR046W_TRM112_DAMP_2


title: YOL124C_TRM11_DEL_2

value: YOL124C deletion pool


title: YOL124C_TRM11_DEL_1


title: WholeBlood_CRC305DGENT0321012_Day7

value: white

value: not american hispanic or latino

value: FLUADD


title: WholeBlood_CRC305DGENT1703047_Day3

value: female

value: whole blood


title: WholeBlood_CRC305DGENT2203041_Day3


title: WholeBlood_CRC305DGENT1643040_Day7


title: WholeBlood_CRC305DGENT1221030_Day1

value: male


title: WholeBlood_CRC305DGENT2281049_Day7


title: WholeBlood_CRC305DGENT0041017_Day1


title: YDR120C_TRM1_DEL_2

value: YDR120C deletion pool


title: WholeBlood_CRC305DGENT0213015_Day21


title: WholeBlood_CRC305DGENT2441054_Day0


title: WholeBlood_CRC305DGENT0273001_Day1


title: WholeBlood_CRC305DGENT2371051_Day21


title: YNL299W_TRF5_DEL_2

value: YNL299W deletion pool


title: YDR120C_TRM1_DEL_1


title: YNL299W_TRF5_DEL_1


title: YDR457W_TOM1_DEL_1

value: YDR457W deletion pool


title: YDR457W_TOM1_DEL_2


title: WholeBlood_CRC305DGENT0333003_Day0


title: YDR395W_SXM1_DEL_4

value: YDR395W deletion pool


title: YDR395W_SXM1_DEL_2

value: Mix of haploid strains derived from BY4742/BY4741


title: YDR395W_SXM1_DEL_3


title: WholeBlood_CRC305DGENT1403026_Day0


title: WholeBlood_CRC305DGENT1563035_Day21


title: YBR069C_TAT1_DEL_1

value: YBR069C deletion pool


title: WholeBlood_CRC305DGENT1313027_Day3


title: YKL081W_TEF4_DEL_1

value: YKL081W deletion pool


title: WholeBlood_CRC305DGENT1271037_Day0


title: YBR069C_TAT1_DEL_2


title: WholeBlood_CRC305DGENT0251006_Day0


title: YOL020W_TAT2_DEL_2

value: YOL020W deletion pool


title: YOL020W_TAT2_DEL_1

value: multiple deletion reference mix


title: WholeBlood_CRC305DGENT0041017_Day21


title: YCR053W_THR4_DEL_1

value: YCR053W deletion pool


title: YCR053W_THR4_DEL_2


title: YKL081W_TEF4_DEL_2


title: WholeBlood_CRC305DGENT1331025_Day0


title: WholeBlood_CRC305DGENT1563035_Day3


title: YDR395W_SXM1_DEL_1

value: YEL068C deletion reference mix


title: WholeBlood_CRC305DGENT0313004_Day1

value: white


title: WholeBlood_CRC305DGENT0321012_Day3

value: not american hispanic or latino


title: WholeBlood_CRC305DGENT2463060_Day0

value: FLUADD


title: WholeBlood_CRC305DGENT1321028_Day21


title: YNL222W_SSU72_TETO2_2

value: YNL222W TETO2 pool


title: WholeBlood_CRC305DGENT1253029_Day21

value: female

value: whole blood


title: WholeBlood_CRC305DGENT0383009_Day7


title: YNL222W_SSU72_TETO2_1


title: WholeBlood_CRC305DGENT0313004_Day0


title: YMR191W_SPG5_DEL_2

value: YMR191W deletion pool


title: snR9_SNR9_DEL_1

value: snR9 deletion pool


title: WholeBlood_CRC305DGENT1493038_Day7


title: WholeBlood_CRC305DGENT1301023_Day3

value: male


title: YCL037C_SRO9_DEL_1

value: YCL037C deletion pool


title: YMR191W_SPG5_DEL_1

value: Mix of haploid strains derived from BY4742/BY4741


title: WholeBlood_CRC305DGENT1423030_Day3


title: MIApaca_ATO_24h

city: Shanghai

first: Congling

last: Xu

address: number 2 ruijin road

country: China

institute: Shanghai Institute of Hematology

hyb_protocol: Fragmented and biotin-labeled cRNA was hybridized to affymetrix human U133 plus 2.0 array chip using the Affymetrix hybridization kit. Arrays were incubated in 45°C hybridization oven for 16 hours,rotating at 60 rpm.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000

data_processing: Raw data were normalized by RMA algorithm

label: biotin

source_name: pancreatic cancer cell line MIApaca

label_protocol: 5 ug of total RNA was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was used to synthesize biotin-labeled cRNA with the IVT kit (Affymetrix, USA). Biotin-labeled cRNA was fragmented according to affymetrix protocol.

growth_protocol: Pancreatic cancer cells PANC-1,BXPC-3 and MIApaca2 were cultured in DMEM with 10%FBS, and ASPC-1 was cultured in 1640 with 10%FBS.

extract_protocol: Cellular RNA was isolated by Tri-Reagent using the manufacturer’s instructions. Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.

treatment_protocol: Pancreatic cancer cells BXPC-3 and MIApaca2 were treated with ATO 2.5μM for 0,6,12,24 and 48 Hours. PANC-1 and ASPC-1 were treated with ATO(2.5μM) alone or combination of ATO(2.5μM) and BRD4 inhibitor JQ1(1μM) for 0,6,24 and 48 hours.

tag: disease state

value: pancreatic cancer

tag: time point

value: ATO

tag: cell line

value: MIApaca


title: snR85_SNR85_DEL_1

value: snR85 deletion pool

value: multiple deletion reference mix


title: snR85_SNR85_DEL_2


title: YCL037C_SRO9_DEL_2


title: snR82_SNR82_DEL_2

value: snR82 deletion pool


title: WholeBlood_CRC305DGENT0291007_Day21

value: white


title: WholeBlood_CRC305DGENT1883049_Day1

value: not american hispanic or latino


title: WholeBlood_CRC305DGENT2391057_Day1

value: FLUADD


title: WholeBlood_CRC305DGENT1691045_Day1


title: MIApaca_control

value: untreated


title: snR82_SNR82_DEL_1


title: snR68_SNR68_DEL_1

value: snR68 deletion pool


title: MIApaca_ATO_6h


title: MIApaca_ATO_48h


title: MIApaca_ATO_12h


title: WholeBlood_CRC305DGENT0191018_Day7

value: whole blood


title: WholeBlood_CRC305DGENT1683046_Day7

value: female


title: snR64_SNR64_DEL_1

value: snR64 deletion pool


title: BXPC3_ATO_48h

source_name: pancreatic cancer cell line BXPC3


title: WholeBlood_CRC305DGENT1411039_Day3

value: male


title: snR49_SNR49_DEL_2

value: snR49 deletion pool


title: BXPC3_ATO_24h


title: snR65_SNR65_DEL_1

value: Mix of haploid strains derived from BY4742/BY4741

value: snR65 deletion pool


title: BXPC3_ATO_12h

value: pancreatic cancer

value: ATO


title: PANC1_ ATO+JQ1_48h

source_name: pancreatic cancer cell line PANC1

value: ATO and JQ1


title: WholeBlood_CRC305DGENT2391057_Day7


title: snR67_SNR67_DEL_1

value: snR67 deletion pool

value: YEL068C deletion reference mix


title: WholeBlood_CRC305DGENT0403011_Day7

value: white


title: WholeBlood_CRC305DGENT0251006_Day7

value: not american hispanic or latino


title: snR49_SNR49_DEL_1


title: WholeBlood_CRC305DGENT1691045_Day3

value: FLUADD


title: WholeBlood_CRC305DGENT2241042_Day1


title: PANC1_ ATO+JQ1_24h


title: WholeBlood_CRC305DGENT0131009_Day3


title: BXPC3_ATO_6h


title: snR46_SNR46_DEL_2

value: snR46 deletion pool

value: multiple deletion reference mix


title: snR37_SNR37_DEL_3

value: snR37 deletion pool


title: WholeBlood_CRC305DGENT2413052_Day21

value: female

value: whole blood


title: snR46_SNR46_DEL_1


title: snR37_SNR37_DEL_2


title: WholeBlood_CRC305DGENT1563035_Day0


title: PANC1_JQ1_48h


title: snR34_SNR34_DEL_2

value: snR34 deletion pool


title: snR35_SNR35_DEL_1

value: snR35 deletion pool


title: PANC1_ ATO+JQ1_6h


title: WholeBlood_CRC305DGENT1341027_Day1

value: male


title: WholeBlood_CRC305DGENT1321028_Day0


title: WholeBlood_CRC305DGENT0181014_Day7


title: PANC1_JQ1_24h


title: BXPC3_control

value: untreated


title: WholeBlood_CRC305DGENT0223019_Day3


title: PANC1_ ATO_48h

value: pancreatic cancer


title: PANC1_ ATO_6h

value: ATO


title: WholeBlood_CRC305DGENT2313050_Day21


title: WholeBlood_CRC305DGENT0021002_Day21


title: PANC1_ ATO_24h


title: WholeBlood_CRC305DGENT0283005_Day7


title: snR34_SNR34_DEL_1

value: Mix of haploid strains derived from BY4742/BY4741


title: snR35_SNR35_DEL_2


title: PANC1_control


title: PANC1_JQ1_6h


title: snR37_SNR37_DEL_1


title: snR33_SNR33_DEL_3

value: snR33 deletion pool


title: ASPC1_ ATO+JQ1_48h

source_name: pancreatic cancer cell line ASPC1

value: ATO and JQ1


title: snR33_SNR33_DEL_2


title: WholeBlood_CRC305DGENT1563035_Day1

value: white


title: WholeBlood_CRC305DGENT2313050_Day0

value: not american hispanic or latino


title: snR3_SNR3_DEL_1

value: snR3 deletion pool

value: YEL068C deletion reference mix


title: ASPC1_ ATO+JQ1_24h


title: snR3_SNR3_DEL_2

value: multiple deletion reference mix


title: YDR510W_SMT3_DAMP_1

value: YDR510W DAMP pool


title: ASPC1_ JQ1_48h


title: ASPC1_ JQ1_6h


title: ASPC1_ ATO+JQ1_6h


title: WholeBlood_CRC305DGENT0171010_Day3

value: FLUADD


title: ASPC1_ ATO_24h


title: WholeBlood_CRC305DGENT0291007_Day0

value: whole blood


title: WholeBlood_CRC305DGENT2381052_Day1


title: YDR510W_SMT3_DAMP_2


title: YGR271W_SLH1_DEL_1

value: YGR271W deletion pool


title: WholeBlood_CRC305DGENT2423054_Day3

value: female


title: WholeBlood_CRC305DGENT2401055_Day1

value: male


title: WholeBlood_CRC305DGENT0233014_Day1


title: ASPC1_ JQ1_24h


title: YIL104C_SHQ1_DAMP_1

value: YIL104C DAMP pool


title: YIL104C_SHQ1_DAMP_2


title: snR9_SNR9_DEL_2

value: snR9 deletion pool


title: WholeBlood_CRC305DGENT0163013_Day7


title: ASPC1_ ATO_6h

value: pancreatic cancer

value: ATO


title: WholeBlood_CRC305DGENT0171010_Day0


title: ASPC1_control

value: untreated


title: BAY1436032+Azacitidine rep 3

city: Hannover

first: Anuhar

last: Chaturvedi

address: Cral Neuberg Strasse-1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

country: Germany

institute: Hannover Medical School

description: Gene expression data from IDH1mut PDX mice treated with BAY1436032+Azacitidine

hyb_protocol: 7.5 µg of biotinylated cRNA were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix GeneChip HG-U133 2.0 for 16 hours at 45°C. Steps for washing and SA-PE staining were processed on the fluidics station 450 using the recommended FS450 protocol (Affymetrix; Santa Clara, CA).

scan_protocol: IImage Analysis was performed on GCS3000 Scanner and GCOS1.2 Software Suite (Affymetrix; Santa Clara, CA).

data_processing: Analysis of microarray data was performed using GeneSpring 11.5.1 software suite (Agilent Technologies, CA, USA). Signal intensities (raw data) were background corrected, normalized and summarized using RMA. Gene expression values per condition are given as log2 relative expression to mean expression value calculated from log2 intensities of all conditions (mean centralization, normalized data). Significance of differential gene expression was calculated by GeneSpring software using error corrected  unpaired T-Test.

source_name: sorted Human CD45+ cells from bone marrow of PDX mouse

label_protocol: 500 ng of total RNA were used for biotin labelling according the 3´ IVT Express Kit (Affymetrix; Santa Clara, CA).

growth_protocol: invivo from NSG mice

extract_protocol: Qiagen Rneasy plus Mini Kit according to manufacturers instructions

treatment_protocol: Human IDH1mut AML patient cells transplantation in NSG mice. Mice were treated either with vehicle, azacitidine (1 mg/kg, s.c., days 1 to 5), BAY1436032 (150 mg/kg, p.o., q.d., 4 weeks) or the simultaneous combination of BAY1436032 and azacitidine. Four weeks after treatment, human CD45+ cells were sorted from mouse bone marrow, from which total RNA was extracted and subjected to microarray analysis.

tag: host

value: NSG mice

value: BAY1436032 (150 mg/kg, p.o., q.d., 4 weeks)+azacitidine (1 mg/kg, s.c., days 1 to 5)


title: WholeBlood_CRC305DGENT1221030_Day0

value: white

value: not american hispanic or latino


title: YLR058C_SHM2_DEL_2

value: Mix of haploid strains derived from BY4742/BY4741

value: YLR058C deletion pool

tag: date


title: snR33_SNR33_DEL_1

value: snR33 deletion pool

tag: screen id

value: YEL068C deletion reference mix


title: WholeBlood_CRC305DGENT1453037_Day7

tag: participant

value: FLUADD

value: whole blood


title: BAY1436032+Azacitidine rep 2


title: YGR271W_SLH1_DEL_2

value: YGR271W deletion pool

value: multiple deletion reference mix


title: WholeBlood_CRC305DGENT1653039_Day21

tag: gender

value: female


title: YLR058C_SHM2_DEL_1


title: WholeBlood_CRC305DGENT1351022_Day7

value: male

tag: age


title: YDR363W-A_SEM1_DEL_1

value: YDR363W-A deletion pool


title: BAY1436032+Azacitidine rep 1


title: YDR363W-A_SEM1_DEL_2


title: YDR143C_SAN1_DEL_2

value: YDR143C deletion pool


title: Azacitidine rep 1

description: Gene expression data from IDH1mut PDX mice treated with Azacitidine

value: azacitidine (1 mg/kg, s.c., days 1 to 5)


title: WholeBlood_CRC305DGENT1233028_Day3

tag: race


title: Azacitidine rep 3

value: NSG mice


title: YDR143C_SAN1_DEL_1


title: BAY1436032 rep 3

description: Gene expression data from IDH1mut PDX mice treated with BAY1436032


title: BAY1436032 rep 2


title: ASPC1_ ATO_48h

value: pancreatic cancer

value: ATO


title: BAY1436032 rep 1


title: YHR087W_RTC3_DEL_2

value: YHR087W deletion pool


title: Azacitidine rep 2


title: WholeBlood_CRC305DGENT0083012_Day3

value: white

tag: ethnicity

value: not american hispanic or latino


title: YOR001W_RRP6_TETO2_2

value: Mix of haploid strains derived from BY4742/BY4741

value: YOR001W TETO2 pool


title: WholeBlood_CRC305DGENT1281024_Day1

tag: protocol

value: FLUADD


title: Vehicle rep 3

description: Gene expression data from IDH1mut PDX mice treated with Vehicle

tag: treatment

value: vehicle


title: YLR264W_RPS28B_DEL_2

value: YLR264W deletion pool


title: Vehicle rep 2


title: YHR087W_RTC3_DEL_1

value: multiple deletion reference mix


title: WholeBlood_CRC305DGENT1603032_Day21

value: female

value: PLACEBOD

tag: day

value: whole blood


title: WholeBlood_CRC305DGENT1643040_Day1

tag: tissue


title: YOR001W_RRP6_TETO2_1

tag: strain

value: YEL068C deletion reference mix


title: YLR264W_RPS28B_DEL_1

tag: genotype


title: WholeBlood_CRC305DGENT1313027_Day7


title: YOR167C_RPS28A_DEL_1

value: YOR167C deletion pool


title: YOR167C_RPS28A_DEL_2


title: YJL191W_RPS14B_DEL_2

value: YJL191W deletion pool


title: YJL191W_RPS14B_DEL_1


title: WholeBlood_CRC305DGENT2391057_Day3

value: male


title: WholeBlood_CRC305DGENT1691045_Day7


title: WholeBlood_CRC305DGENT2273043_Day21


title: WholeBlood_CRC305DGENT0411008_Day0


title: Vehicle rep 1

value: NSG mice


title: YCR031C_RPS14A_DEL_2

value: YCR031C deletion pool


title: WholeBlood_CRC305DGENT1573034_Day7

value: white


title: WholeBlood_CRC305DGENT1243023_Day3

value: not american hispanic or latino


title: WholeBlood_CRC305DGENT2211046_Day1


title: WholeBlood_CRC305DGENT1351022_Day3


title: YDL020C_RPN4_DEL_2

value: Mix of haploid strains derived from BY4742/BY4741

value: YDL020C deletion pool


title: WholeBlood_CRC305DGENT1433024_Day1

value: FLUADD


title: YCR031C_RPS14A_DEL_1


title: YDL020C_RPN4_DEL_1


title: YGL004C_RPN14_DEL_2

value: YGL004C deletion pool


title: YHR200W_RPN10_DEL_1

value: YHR200W deletion pool


title: YGL147C_RPL9A_DEL_2

value: YGL147C deletion pool

value: multiple deletion reference mix


title: WholeBlood_CRC305DGENT1291026_Day21


title: YPL198W_RPL7B_DEL_2

value: YPL198W deletion pool


title: YGL004C_RPN14_DEL_1


title: YHR200W_RPN10_DEL_2


title: YGL147C_RPL9A_DEL_1


title: YPL198W_RPL7B_DEL_1


title: YDR500C_RPL37B_DEL_2

value: YDR500C deletion pool


title: YDR500C_RPL37B_DEL_1


title: WholeBlood_CRC305DGENT0021002_Day0

value: whole blood


title: WholeBlood_CRC305DGENT2371051_Day1


title: WholeBlood_CRC305DGENT2193048_Day7

value: female


title: WholeBlood_CRC305DGENT2361060_Day7


title: WholeBlood_CRC305DGENT2371051_Day7


title: YLR185W_RPL37A_DEL_1

value: YLR185W deletion pool


title: WholeBlood_CRC305DGENT1221030_Day3

value: male


title: WholeBlood_CRC305DGENT1471032_Day1


title: WholeBlood_CRC305DGENT0233014_Day3


title: WholeBlood_CRC305DGENT1773058_Day3


title: WholeBlood_CRC305DGENT0083012_Day1


title: WholeBlood_CRC305DGENT0171010_Day7


title: YGR148C_RPL24B_DEL_1

value: YGR148C deletion pool

value: YEL068C deletion reference mix


title: WholeBlood_CRC305DGENT0233014_Day0

value: white


title: YGR148C_RPL24B_DEL_2


title: YDR418W_RPL12B_DEL_1

value: YDR418W deletion pool


title: WholeBlood_CRC305DGENT1643040_Day21

value: not american hispanic or latino


title: YCL028W_RNQ1_DEL_1

value: Mix of haploid strains derived from BY4742/BY4741

value: YCL028W deletion pool


title: YMR239C_RNT1_TETO2_2

value: YMR239C TETO2 pool


title: YDR418W_RPL12B_DEL_2


title: WholeBlood_CRC305DGENT0171010_Day21

value: FLUADD


title: WholeBlood_CRC305DGENT0251006_Day3


title: YNL072W_RNH201_DEL_2

value: YNL072W deletion pool


title: YCL028W_RNQ1_DEL_2

value: multiple deletion reference mix


title: YMR283C_RIT1_DEL_2

value: YMR283C deletion pool


title: WholeBlood_CRC305DGENT2433059_Day0


title: WholeBlood_CRC305DGENT1703047_Day21

value: PLACEBOD


title: YNL072W_RNH201_DEL_1


title: YMR283C_RIT1_DEL_1


title: YMR239C_RNT1_TETO2_1


title: WholeBlood_CRC305DGENT1831059_Day7

value: whole blood


title: WholeBlood_CRC305DGENT1773058_Day21

value: female


title: WholeBlood_CRC305DGENT0153020_Day1


title: WholeBlood_CRC305DGENT1281024_Day7


title: WholeBlood_CRC305DGENT1603032_Day0


title: YLR107W_REX3_DEL_2

value: YLR107W deletion pool


title: WholeBlood_CRC305DGENT0273001_Day0


title: WholeBlood_CRC305DGENT2211046_Day7

value: male


title: WholeBlood_CRC305DGENT1643040_Day0


title: YLR059C_REX2_DEL_2

value: YLR059C deletion pool


title: YLR059C_REX2_DEL_1

value: YEL068C deletion reference mix


title: YMR075W_RCO1_DEL_2

value: YMR075W deletion pool


title: WholeBlood_CRC305DGENT0251006_Day1

value: white


title: WholeBlood_CRC305DGENT0421004_Day3

value: not american hispanic or latino


title: WholeBlood_CRC305DGENT2463060_Day3


title: WholeBlood_CRC305DGENT1623033_Day3


title: YMR075W_RCO1_DEL_1

value: Mix of haploid strains derived from BY4742/BY4741


title: YOR048C_RAT1_TETO2_2

value: YOR048C TETO2 pool


title: YOR048C_RAT1_TETO2_1


title: WholeBlood_CRC305DGENT1371020_Day7


title: WholeBlood_CRC305DGENT0083012_Day21


title: YLR107W_REX3_DEL_1


title: YGL246C_RAI1_DEL_2

value: YGL246C deletion pool


title: YGL246C_RAI1_DEL_1


title: YNL250W_RAD50_DEL_2

value: YNL250W deletion pool


title: YNL250W_RAD50_DEL_1


title: YPL212C_PUS1_DEL_4

value: YPL212C deletion pool


title: WholeBlood_CRC305DGENT1511040_Day0


title: WholeBlood_CRC305DGENT1671048_Day1


title: WholeBlood_CRC305DGENT0283005_Day21

value: FLUADD


title: WholeBlood_CRC305DGENT0393007_Day0


title: WholeBlood_CRC305DGENT0051016_Day21


title: WholeBlood_CRC305DGENT1721053_Day0


title: WholeBlood_CRC305DGENT1313027_Day1


title: YPL212C_PUS1_DEL_2


title: YPL212C_PUS1_DEL_3

value: multiple deletion reference mix


title: YPL212C_PUS1_DEL_1


title: WholeBlood_CRC305DGENT2233045_Day1


title: YGR135W_PRE9_DEL_1

value: YGR135W deletion pool


title: YGR135W_PRE9_DEL_2


title: YPL144W_POC4_DEL_2

value: YPL144W deletion pool


title: YDL006W_PTC1_DEL_2

value: YDL006W deletion pool


title: YBL051C_PIN4_DEL_2

value: YBL051C deletion pool


title: WholeBlood_CRC305DGENT0343002_Day3

value: female

value: whole blood


title: WholeBlood_CRC305DGENT1831059_Day0

value: male


title: YPL144W_POC4_DEL_1

value: YEL068C deletion reference mix


title: YBL051C_PIN4_DEL_1


title: YLR185W_RPL37A_DEL_2

value: YLR185W deletion pool


title: YDR228C_PCF11_DAMP_2

value: YDR228C DAMP pool


title: WholeBlood_CRC305DGENT1341027_Day3

value: white

value: not american hispanic or latino


title: YNL097C_PHO23_DEL_1

value: Mix of haploid strains derived from BY4742/BY4741

value: YNL097C deletion pool


title: WholeBlood_CRC305DGENT2211046_Day21


title: YDL006W_PTC1_DEL_1


title: WholeBlood_CRC305DGENT0083012_Day0


title: WholeBlood_CRC305DGENT0361005_Day21


title: WholeBlood_CRC305DGENT2331050_Day3


title: WholeBlood_CRC305DGENT1653039_Day1


title: YNL097C_PHO23_DEL_2


title: WholeBlood_CRC305DGENT2331050_Day1


title: WholeBlood_CRC305DGENT2233045_Day3


title: WholeBlood_CRC305DGENT1471032_Day3


title: WholeBlood_CRC305DGENT1351022_Day1


title: WholeBlood_CRC305DGENT1403026_Day3


title: YDR228C_PCF11_DAMP_1


title: WholeBlood_CRC305DGENT1403026_Day7


title: WholeBlood_CRC305DGENT0141011_Day3


title: YJL128C_PBS2_DEL_2

value: YJL128C deletion pool


title: YJL128C_PBS2_DEL_1


title: YKL025C_PAN3_DEL_2

value: YKL025C deletion pool


title: YGL094C_PAN2_DEL_2

value: YGL094C deletion pool

value: multiple deletion reference mix


title: YFL044C_OTU1_DEL_2

value: YFL044C deletion pool


title: YGL094C_PAN2_DEL_1


title: YFL044C_OTU1_DEL_1


title: WholeBlood_CRC305DGENT0403011_Day1

value: FLUADD


title: WholeBlood_CRC305DGENT2463060_Day21


title: WholeBlood_CRC305DGENT1393025_Day21

value: PLACEBOD


title: YBR094W_PBY1_DEL_1

value: YBR094W deletion pool


title: YKL025C_PAN3_DEL_1


title: YDR067C_OCA6_DEL_2

value: YDR067C deletion pool


title: YDR067C_OCA6_DEL_1


title: YHL029C_OCA5_DEL_1

value: YHL029C deletion pool


title: YHL029C_OCA5_DEL_2


title: YNL056W_OCA2_DEL_2

value: YNL056W deletion pool


title: YHL020C_OPI1_DEL_2

value: YHL020C deletion pool


title: WholeBlood_CRC305DGENT1851047_Day7

value: male

value: whole blood


title: YNL099C_OCA1_DEL_2

value: YNL099C deletion pool


title: WholeBlood_CRC305DGENT1521035_Day1

value: white

value: not american hispanic or latino


title: YNL056W_OCA2_DEL_1

value: Mix of haploid strains derived from BY4742/BY4741


title: YNL099C_OCA1_DEL_1


title: WholeBlood_CRC305DGENT0103017_Day21

value: female


title: YHL020C_OPI1_DEL_1


title: WholeBlood_CRC305DGENT1721053_Day1


title: WholeBlood_CRC305DGENT1643040_Day3


title: WholeBlood_CRC305DGENT2441054_Day21


title: WholeBlood_CRC305DGENT0383009_Day1


title: WholeBlood_CRC305DGENT1721053_Day7


title: WholeBlood_CRC305DGENT1541033_Day7


title: YMR153W_NUP53_DEL_2

value: YMR153W deletion pool


title: WholeBlood_CRC305DGENT1453037_Day21


title: WholeBlood_CRC305DGENT1493038_Day21


title: WholeBlood_CRC305DGENT1493038_Day0


title: WholeBlood_CRC305DGENT1611036_Day21


title: WholeBlood_CRC305DGENT2321056_Day7


title: YMR153W_NUP53_DEL_1

value: YEL068C deletion reference mix


title: WholeBlood_CRC305DGENT2221043_Day7


title: WholeBlood_CRC305DGENT0073006_Day1


title: YLR197W_NOP56_DAMP_2

value: YLR197W DAMP pool

value: multiple deletion reference mix


title: YJL208C_NUC1_DEL_2

value: YJL208C deletion pool


title: YHL023C_NPR3_DEL_1

value: YHL023C deletion pool


title: YHL023C_NPR3_DEL_2


title: YDL213C_NOP6_DEL_1

value: YDL213C deletion pool


title: YOR310C_NOP58_DAMP_1

value: YOR310C DAMP pool


title: YOR310C_NOP58_DAMP_2


title: YJL208C_NUC1_DEL_1


title: YDL014W_NOP1_DAMP_2

value: YDL014W DAMP pool


title: YDL014W_NOP1_DAMP_1


title: YLR197W_NOP56_DAMP_1


title: WholeBlood_CRC305DGENT0361005_Day0

value: FLUADD


title: WholeBlood_CRC305DGENT0073006_Day0


title: WholeBlood_CRC305DGENT0123021_Day1


title: WholeBlood_CRC305DGENT1721053_Day21

value: male


title: WholeBlood_CRC305DGENT0041017_Day0

value: whole blood


title: WholeBlood_CRC305DGENT1541033_Day1


title: YDL213C_NOP6_DEL_2


title: YPL093W_NOG1_DAMP_2

value: YPL093W DAMP pool


title: WholeBlood_CRC305DGENT0283005_Day1

value: white


title: WholeBlood_CRC305DGENT2433059_Day7

value: not american hispanic or latino


title: WholeBlood_CRC305DGENT2221043_Day21


title: WholeBlood_CRC305DGENT2241042_Day7


title: YDL014W_NOP1_DAMP_3

value: Mix of haploid strains derived from BY4742/BY4741


title: WholeBlood_CRC305DGENT0393007_Day7

value: female


title: WholeBlood_CRC305DGENT0011001_Day0


title: WholeBlood_CRC305DGENT1541033_Day3


title: YPL093W_NOG1_DAMP_1


title: YLR363C_NMD4_DEL_1

value: YLR363C deletion pool


title: YHR077C_NMD2_DEL_2

value: YHR077C deletion pool


title: YHR077C_NMD2_DEL_1


title: WholeBlood_CRC305DGENT1883049_Day3


title: WholeBlood_CRC305DGENT1461019_Day0


title: WholeBlood_CRC305DGENT1411039_Day1


title: YDL208W_NHP2_DAMP_2

value: YDL208W DAMP pool


title: WholeBlood_CRC305DGENT2203041_Day0


title: WholeBlood_CRC305DGENT1243023_Day21


title: YIL007C_NAS2_DEL_2

value: YIL007C deletion pool

value: multiple deletion reference mix


title: YDL208W_NHP2_DAMP_1

value: YEL068C deletion reference mix


title: YIL007C_NAS2_DEL_1


title: YKR048C_NAP1_DEL_2

value: YKR048C deletion pool


title: YGR232W_NAS6_DEL_1

value: YGR232W deletion pool


title: YGR232W_NAS6_DEL_2


title: YKR048C_NAP1_DEL_1


title: YMR080C_NAM7_DEL_1

value: YMR080C deletion pool


title: YDR140W_MTQ2_DAMP_1

value: YDR140W DAMP pool

value: YPR014C deletion reference mix


title: YHR086W_NAM8_DEL_2

value: YHR086W deletion pool


title: WholeBlood_CRC305DGENT2413052_Day1

value: FLUADD

value: whole blood


title: YMR080C_NAM7_DEL_2


title: WholeBlood_CRC305DGENT0141011_Day21

value: male

value: white

value: not american hispanic or latino


title: WholeBlood_CRC305DGENT0213015_Day0

value: female


title: YHR086W_NAM8_DEL_1

value: Mix of haploid strains derived from BY4742/BY4741


title: WholeBlood_CRC305DGENT1683046_Day21


title: WholeBlood_CRC305DGENT0051016_Day0


title: WholeBlood_CRC305DGENT1521035_Day21


title: WholeBlood_CRC305DGENT1253029_Day1


title: WholeBlood_CRC305DGENT1211029_Day3


title: YBR255W_MTC4_DEL_3

value: YBR255W deletion pool


title: WholeBlood_CRC305DGENT0103017_Day3


title: WholeBlood_CRC305DGENT0203018_Day0


title: WholeBlood_CRC305DGENT0021002_Day1


title: WholeBlood_CRC305DGENT0141011_Day7


title: WholeBlood_CRC305DGENT2361060_Day0


title: TKO_5mC

type: SRA

city: shanghai

first: Yujiang

middle: Geno

last: Shi

address: 131 Dong An Road

department: Institute of Biomedical Science

institute: Fudan university

library_source: genomic

data_processing:
The MeDIP-seq reads were mapped to the human genome (hg19) using Bowtie1.0.0
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: hg19
Supplementary_files_format_and_content: Genome coverage bigwig files

source_name: TKO cells

growth_protocol: Cells were cultured in were cultured in RPMI1640 supplemented with 10% fetal bovine serum (ATCC).

extract_protocol:
MeDIP-seq was performed according to the previous study (Li Tan, 2013. doi: 10.1093/nar/gkt091).
MeDIP DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: multiple myeloma model

tag: genotype/variation

value: NSD2 translocation knockout

tag: antibody

value: 5mC (Active Motif, #39649)


title: TKO_H3K36me2 ChIP-seq

data_processing:
The ChIP-seq reads were mapped to the human genome (hg19) using Bowtie1.0.0
PCR duplicates were removed using samtools (v1.7) rmdup.
Genome coverage bigwig files were generated by deeptools (v 3.0.2) bamCoverage with the parameter “--normalizeUsing RPKM --binSize 5”.
Genome_build: hg19
Supplementary_files_format_and_content: Genome coverage bigwig files

extract_protocol:
Chromatin samples were incubated with specific antibodies in ChIP Lysis buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 1%Triton, 0.1%Na-deoxylcholate, 0.1% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on protein A/G beads (10μl per reaction). The bound fractions were washed 3 times with Lysis buffer, and 3 times with RIPA buffer (50mM Hepes, 300mM LiCl, 1mM EDTA, 0.5%NP-40, 0.7%Nadeoxylcholate), and once with TE. Elution and Reverse crosslinking were carried out in Elution buffer (50mM Tris, PH8.0, 1mM EDTA, 1% SDS) 65℃ for 6 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR extraction kit (QIAGEN).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line


title: YMR037C_MSN2_DEL_2

value: YMR037C deletion pool

tag: date

value: multiple deletion reference mix


title: WholeBlood_CRC305DGENT1253029_Day7


title: YBR255W_MTC4_DEL_2

tag: screen id


title: YPL184C_MRN1_DEL_1

value: YPL184C deletion pool


title: WholeBlood_CRC305DGENT1403026_Day1

tag: participant


title: YOR274W_MOD5_DEL_2

value: YOR274W deletion pool


title: KMS11_H3K36me2 ChIP-seq

source_name: KMS11 cells

value: Parental


title: KMS11_5mC


title: YMR037C_MSN2_DEL_1


title: YOR274W_MOD5_DEL_1

value: YEL068C deletion reference mix


title: WholeBlood_CRC305DGENT1483036_Day0

tag: gender

value: FLUADD


title: WholeBlood_CRC305DGENT0181014_Day1

tag: age

value: whole blood


title: WholeBlood_CRC305DGENT0123021_Day3

tag: race


title: WholeBlood_CRC305DGENT1823053_Day3

tag: ethnicity


title: YPR051W_MAK3_DEL_3

value: YPR051W deletion pool


title: WholeBlood_CRC305DGENT1823053_Day7

value: white

tag: protocol


title: YPR051W_MAK3_DEL_1


title: YDR005C_MAF1_DEL_2

value: YDR005C deletion pool


title: YDR005C_MAF1_DEL_1


title: YPL184C_MRN1_DEL_2


title: WholeBlood_CRC305DGENT1631034_Day1

value: male

value: not american hispanic or latino

tag: treatment


title: WholeBlood_CRC305DGENT0223019_Day0

value: female

tag: day


title: YBR255W_MTC4_DEL_1

value: Mix of haploid strains derived from BY4742/BY4741

value: YBR255W deletion pool


title: WholeBlood_CRC305DGENT0373010_Day1

tag: tissue


title: WholeBlood_CRC305DGENT1453037_Day1


title: YNR050C_LYS9_DEL_1

tag: strain

value: YNR050C deletion pool


title: YHR121W_LSM12_DEL_2

tag: genotype

value: YHR121W deletion pool


title: WholeBlood_CRC305DGENT0111015_Day21


title: YHR121W_LSM12_DEL_1

value: multiple deletion reference mix


title: WholeBlood_CRC305DGENT1851047_Day1

value: PLACEBOD


title: YJR070C_LIA1_DEL_2

value: YJR070C deletion pool


title: WholeBlood_CRC305DGENT2273043_Day7


title: WholeBlood_CRC305DGENT1313027_Day21


title: WholeBlood_CRC305DGENT2233045_Day21


title: YNR050C_LYS9_DEL_2


title: WholeBlood_CRC305DGENT0213015_Day7


title: YOR304W_ISW2_DEL_2

value: YOR304W deletion pool


title: WholeBlood_CRC305DGENT1423030_Day21


title: WholeBlood_CRC305DGENT1411039_Day7


title: YJR070C_LIA1_DEL_1


title: YOR304W_ISW2_DEL_1

value: YEL068C deletion reference mix


title: YPR051W_MAK3_DEL_2


title: WholeBlood_CRC305DGENT1541033_Day0

value: FLUADD


title: WholeBlood_CRC305DGENT1423030_Day1

value: whole blood


title: WholeBlood_CRC305DGENT2343042_Day1


title: YKR019C_IRS4_DEL_1

value: YKR019C deletion pool


title: WholeBlood_CRC305DGENT2321056_Day3

value: white


title: WholeBlood_CRC305DGENT1671048_Day0


title: YOR235W_IRC13_DEL_1

value: YOR235W deletion pool


title: YLR021W_IRC25_DEL_2

value: YLR021W deletion pool


title: WholeBlood_CRC305DGENT0163013_Day21

value: not american hispanic or latino


title: WholeBlood_CRC305DGENT1631034_Day0

value: male


title: YGL141W_HUL5_DEL_2

value: Mix of haploid strains derived from BY4742/BY4741

value: YGL141W deletion pool


title: WholeBlood_CRC305DGENT0181014_Day3


title: WholeBlood_CRC305DGENT2331050_Day21


title: YML058W-A_HUG1_DEL_2

value: YML058W-A deletion pool


title: WholeBlood_CRC305DGENT1843044_Day0

value: female


title: YML058W-A_HUG1_DEL_1

value: multiple deletion reference mix


title: WholeBlood_CRC305DGENT0021002_Day7


title: WholeBlood_CRC305DGENT2203041_Day7


title: YOL012C_HTZ1_DEL_1

value: YOL012C deletion pool


title: WholeBlood_CRC305DGENT0313004_Day7


title: YGL141W_HUL5_DEL_1


title: YOL012C_HTZ1_DEL_2


title: YLR021W_IRC25_DEL_1


title: WholeBlood_CRC305DGENT0213015_Day1


title: WholeBlood_CRC305DGENT1511040_Day21

value: PLACEBOD


title: WholeBlood_CRC305DGENT0321012_Day1


title: YOL013C_HRD1_DEL_2

value: YOL013C deletion pool


title: WholeBlood_CRC305DGENT0373010_Day0


title: YBL002W_HTB2_DEL_1

value: YBL002W deletion pool


title: YBL002W_HTB2_DEL_2


title: YOR235W_IRC13_DEL_2


title: YNL021W_HDA1_DEL_2

value: YNL021W deletion pool


title: YNL021W_HDA1_DEL_1


title: YOL013C_HRD1_DEL_1


title: WholeBlood_CRC305DGENT1551038_Day0

value: FLUADD

value: whole blood


title: YKR084C_HBS1_DEL_1

value: YKR084C deletion pool


title: YKR084C_HBS1_DEL_2


title: YLR192C_HCR1_DEL_2

value: YLR192C deletion pool


title: WholeBlood_CRC305DGENT2423054_Day1

value: white


title: YLR192C_HCR1_DEL_1


title: YEL003W_GIM4_DEL_2

value: YEL003W deletion pool


title: WholeBlood_CRC305DGENT0263008_Day0

value: not american hispanic or latino


title: WholeBlood_CRC305DGENT1721053_Day3

value: male


title: YEL003W_GIM4_DEL_1

value: Mix of haploid strains derived from BY4742/BY4741


title: WholeBlood_CRC305DGENT0411008_Day1


title: WholeBlood_CRC305DGENT2413052_Day0


title: WholeBlood_CRC305DGENT1803057_Day7


title: YEL009C_GCN4_DEL_2

value: YEL009C deletion pool


title: YEL009C_GCN4_DEL_1


title: YDL100C_GET3_DEL_1

value: YDL100C deletion pool


title: WholeBlood_CRC305DGENT0273001_Day7

value: female


title: YDL100C_GET3_DEL_2

value: multiple deletion reference mix


title: WholeBlood_CRC305DGENT1393025_Day3

value: PLACEBOD


title: YDR283C_GCN2_DEL_2

value: YDR283C deletion pool


title: WholeBlood_CRC305DGENT1291026_Day1


title: WholeBlood_CRC305DGENT1671048_Day21


title: WholeBlood_CRC305DGENT1271037_Day21


title: WholeBlood_CRC305DGENT2281049_Day3


title: WholeBlood_CRC305DGENT1291026_Day7


title: YDR283C_GCN2_DEL_1


title: WholeBlood_CRC305DGENT0351013_Day21


title: YCR076C_FUB1_DEL_3

value: YCR076C deletion pool


title: WholeBlood_CRC305DGENT1423030_Day0


title: YCR076C_FUB1_DEL_1


title: YCR076C_FUB1_DEL_2


title: WholeBlood_CRC305DGENT0343002_Day0


title: YLR449W_FPR4_DEL_2

value: YLR449W deletion pool


title: YML074C_FPR3_DEL_3

value: YML074C deletion pool


title: YML074C_FPR3_DEL_2


title: WholeBlood_CRC305DGENT2281049_Day21

value: FLUADD

value: whole blood


title: YLR449W_FPR4_DEL_1


title: YML074C_FPR3_DEL_1

value: YEL068C deletion reference mix


title: YLR342W_FKS1_DEL_1

value: YLR342W deletion pool


title: YMR219W_ESC1_DEL_2

value: YMR219W deletion pool


title: WholeBlood_CRC305DGENT1211029_Day21

value: white

value: not american hispanic or latino


title: YLR342W_FKS1_DEL_2

value: Mix of haploid strains derived from BY4742/BY4741


title: YIL005W_EPS1_DEL_2

value: YIL005W deletion pool


title: WholeBlood_CRC305DGENT1851047_Day3

value: male


title: WholeBlood_CRC305DGENT1411039_Day0


title: WholeBlood_CRC305DGENT1593031_Day21

value: female


title: WholeBlood_CRC305DGENT0321012_Day21


title: WholeBlood_CRC305DGENT0131009_Day1


title: WholeBlood_CRC305DGENT1243023_Day7


title: WholeBlood_CRC305DGENT0411008_Day3


title: PC3-ShRNA-1 (UTR)

city: SIngapore

first: Suhail Ahmed Kabeer

last: Rasheed

address: 8 College Road

department: Programme in Cancer and Stem Cell Biology

country: Singapore

institute: Duke-NUS Medical School

description:
TN1611R1862
This line shows 80-90% knockdown of GNA13.
processed data file: genes.fpkm_tracking

library_source: transcriptomic

data_processing:
Fastqc V0.11.3 was used to check the quality of the bases in the reads.
Sequence reads were mapped to hg38 reference genome using STAR 2.5.1b aligner and BAM files were generated.
The aligned reads were assembled and estimated their abundance in FPKM using Cufflinks 2.1.1.
Further analysed for differential gene expression via Cuffdiff v2.2.1.
Genome_build: hg38
Supplementary_files_format_and_content: *_genes.fpkm_tracking: Tab-delimited files with FPKM values for each sample.

source_name: human prostate cancer

growth_protocol: The cells were grown in DMEM growth media containing 10% FBS and 10 ug/ml Blasticidine (selection marker for shRNA plasmids) in a standard mammalian cell culture CO2 incubator.

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The cells were transfected with the respective control or shRNA plasmids and selected with 20ug/ml Blasticidine for 3 weeks to select for cells stably expressing shRNA control or either of the shRNAs targeting GNA13. Knockdown efficiency was verified using Western blotting for GNA13.

tag: cell type

value: Prostate cancer cells stably expressing shRNA targeting GNA13

tag: shRNA

value: SHRN-UTR


title: WholeBlood_CRC305DGENT0263008_Day3


title: WholeBlood_CRC305DGENT1321028_Day3


title: YDR385W_EFT2_DEL_2

value: YDR385W deletion pool

value: multiple deletion reference mix


title: WholeBlood_CRC305DGENT2453055_Day0


title: PC3-ShRNA-1 (600)

description:
TN1611R1861
This line shows 50-60% knockdown of GNA13.
processed data file: genes.fpkm_tracking


title: WholeBlood_CRC305DGENT1703047_Day1

value: PLACEBOD


title: PC3-ShRNA-Control

description:
TN1611R1860
This line is used as a control and expresses good amount of GNA13.
processed data file: genes.fpkm_tracking

value: Prostate cancer cells stably expressing shRNA control vector alone

value: SHRNA-CONTROL


title: YDR385W_EFT2_DEL_1


title: YER035W_EDC2_DEL_1

value: YER035W deletion pool


title: YKR019C_IRS4_DEL_2

value: YKR019C deletion pool


title: WholeBlood_CRC305DGENT0273001_Day21

value: FLUADD

value: whole blood


title: YBR281C_DUG2_DEL_2

value: YBR281C deletion pool


title: WholeBlood_CRC305DGENT1253029_Day3

value: white

value: not american hispanic or latino


title: YIL005W_EPS1_DEL_1

value: Mix of haploid strains derived from BY4742/BY4741

value: YIL005W deletion pool


title: YBR281C_DUG2_DEL_1

value: YEL068C deletion reference mix


title: YMR162C_DNF3_DEL_1

value: YMR162C deletion pool


title: YMR162C_DNF3_DEL_2


title: YHR115C_DMA1_DEL_2

value: YHR115C deletion pool


title: WholeBlood_CRC305DGENT1831059_Day3

value: male


title: WholeBlood_CRC305DGENT1331025_Day7


title: WholeBlood_CRC305DGENT0153020_Day21

value: female


title: WholeBlood_CRC305DGENT2313050_Day1


title: WholeBlood_CRC305DGENT0041017_Day3


title: WholeBlood_CRC305DGENT2281049_Day0


title: YPR119W_CLB2_DEL_1

value: YPR119W deletion pool

value: multiple deletion reference mix


title: YPR119W_CLB2_DEL_2


title: YPL200W_CSM4_DEL_1

value: YPL200W deletion pool


title: YMR219W_ESC1_DEL_1

value: YMR219W deletion pool


title: YHR115C_DMA1_DEL_1


title: YPL200W_CSM4_DEL_2


title: WholeBlood_CRC305DGENT2273043_Day3


title: EM_CD8-T cells

city: New Haven

first: Insoo

last: Kang

address: 300 Cedar Street

country: USA

institute: Yale University

description: single cell mRNA

data_processing:
Sequencing data was generated on Illumina HiSeq 2500 instrument, same as GSE109535.
Casava 1.8.2 and bcl2fastq2 v2.19.0 were used for fastq generation.
Sequenced reads were trimmed for adaptor sequence, preprocessed for cell barcodes and unique molecular index, and  then mapped to hg38 genome(STAR v2.5.2b).
R1 contains the cell barcode (bp 1-12) and UMI (bp 13-20).
R2 is the biological read.
Genome_build: hg38
Supplementary_files_format_and_content: Text files of expression matrix used in analysis.  The Seurat package (V2.3.0) in R (V3.4.1) was applied to identify differentially expressed genes among 2053 single cells. Cells were considered in the analysis only if they met the following quality control criteria: low expression of mitochondrial genes (<10% of total counts in a cell). The name of each column indicates the cell barcode. For example, the column name "GATTAAGAAGTC" represents the mRNA expression data from the cell "GATTAAGAAGTC".

source_name: Effector memory CD8 T cell

extract_protocol:
Human efffector memory CD8+ T cells were loaded to a microwell-based chip (sc-FTDseq) for mRNA capture by uniquely barcoded beads. The cells were lysed using three cycles of freeze-thaw .
The single cell mRNA libraries were prepared using the DropSeq protocol (GSE63473), tagged with Illumina nextera single indexes (N701, N702, N703, N704, N705, N706). We used the same protocol as in scFTD-seq(GSE109535), where each mRNA captured was end-paired with an unique molecular index(UMI) and a cell barcode.

value: Effector memory CD8 T cell

value: Blood


title: WholeBlood_CRC305DGENT0153020_Day3

value: FLUADD

value: whole blood


title: WholeBlood_CRC305DGENT2441054_Day7

value: white


title: YLR175W_CBF5_DAMP_3

value: YLR175W DAMP pool


title: WholeBlood_CRC305DGENT0383009_Day21

value: not american hispanic or latino


title: WholeBlood_CRC305DGENT0163013_Day1


title: YLR175W_CBF5_DAMP_2

value: Mix of haploid strains derived from BY4742/BY4741


title: YLR175W_CBF5_DAMP_1

value: YEL068C deletion reference mix


title: YKL007W_CAP1_DEL_1

value: YKL007W deletion pool


title: YER048C_CAJ1_DEL_1

value: YER048C deletion pool


title: YER048C_CAJ1_DEL_2


title: YDL175C_AIR2_DEL_1

value: YDL175C deletion pool


title: WholeBlood_CRC305DGENT1403026_Day21

value: female


title: WholeBlood_CRC305DGENT0203018_Day21


title: YMR300C_ADE4_DEL_1

value: YMR300C deletion pool


title: WholeBlood_CRC305DGENT0083012_Day7


title: WholeBlood_CRC305DGENT1493038_Day1


title: YKL206C_ADD66_DEL_2

value: YKL206C deletion pool


title: WholeBlood_CRC305DGENT1683046_Day3


title: YMR300C_ADE4_DEL_2

value: multiple deletion reference mix


title: WholeBlood_CRC305DGENT0051016_Day3

value: male


title: WholeBlood_CRC305DGENT1211029_Day0


title: WholeBlood_CRC305DGENT2233045_Day7


title: WholeBlood_CRC305DGENT1551038_Day3


title: YKL206C_ADD66_DEL_1


title: YMR184W_ADD37_DEL_1

value: YMR184W deletion pool


title: WholeBlood_CRC305DGENT2331050_Day0


title: WholeBlood_CRC305DGENT0063016_Day21


title: WholeBlood_CRC305DGENT1281024_Day3


title: WholeBlood_CRC305DGENT2221043_Day3


title: YMR184W_ADD37_DEL_3


title: WholeBlood_CRC305DGENT0291007_Day7


title: YMR184W_ADD37_DEL_2


title: WholeBlood_CRC305DGENT1393025_Day1

value: PLACEBOD


title: WholeBlood_CRC305DGENT0333003_Day21

value: FLUADD


title: WholeBlood_CRC305DGENT0191018_Day0

value: whole blood


title: WholeBlood_CRC305DGENT2313050_Day3

value: white


title: WholeBlood_CRC305DGENT0403011_Day3


title: WholeBlood_CRC305DGENT1271037_Day1


title: WholeBlood_CRC305DGENT2381052_Day0


title: WholeBlood_CRC305DGENT1301023_Day0


title: WholeBlood_CRC305DGENT1433024_Day0


title: WholeBlood_CRC305DGENT0373010_Day21


title: input DNA HU 2

city: Montpellier

first: Daniel

last: Fisher

address: 1919 Route de Mende

department: IGMM

institute: CNRS

description: control after HU release

data_processing:
Basecalls were performed using the Illumina RTA program.
Demultiplexing was performed using bcl2fastq. Quality control was performed using FastQC, and contaminant verification using FastQ Screen
Sequence reads were mapped to the human genome (hg38) using bowtie2 with default settings
ChIP-Seq read enriched regions (peaks) were identified relative to control Input DNA using MACS2 software
Data were visualised and wig files created using the R package Pasha (Fenouillet, 2015)
Genome_build: hg38

growth_protocol: U2OS cells were grown exponentially in DMEM Glutamax medium with 10% FBS

extract_protocol:
Native chromatin, digested with MNase was pre-cleared, SDS was added to 0.1% and incubated on ice for 12 min. IP buffer with inhibitors was added to 1x concentration (20 mM Tris pH 8.1, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100). After storing 10% of the material for Input sample, aliquots were made and H3S57 antibody (8 μg) (each ChIP with approximately 10M cells) and incubated for 14 h with rotation at 4°C. Pre-washed 20 μl beads slurry per sample (Dynabeads protein A) pre-blocked in 5 mg/ml BSA in PBS were incubated and incubated for 2 h. The beads were washed with a total of 3 ml of each: wash A (50 mM Tris, 10 mM EDTA, 75 mM NaCl), wash B (wash A but with 125 mM NaCl), and wash C (wash A but with 175 mM NaCl). Bound nucleosomes were washed one last time with TE buffer containing 50 mM NaCl before being eluted with 300 μl elution buffer. RNAase was added to digest RNA for 2 h and Proteinase K to digest proteins for another 2 h at 37oC. DNA (from IP and Input samples) was precipitated and cleaned-up with phenol/chloroform/isomylalcohol and Qiagen clean-up columns.
DNA concentration was estimated by Qubit fluorometry and libraries were prepared using the Illumina’s TruSeq ChIP Sample Prep Kit (Low Throughput) according to the manufacture's protocol.
Libraries were multiplexed 12 per lane on a HiSeq2500 Illumina sequencing machine and sequenced in paired-end mode using the TruSeq Rapid SBS kit

value: Osteosarcoma cell line

tag: chip antibody

value: 2mM hydroxyurea for 2 hours


title: WholeBlood_CRC305DGENT1521035_Day3

value: not american hispanic or latino


title: WholeBlood_CRC305DGENT1433024_Day3


title: WholeBlood_CRC305DGENT1631034_Day3


title: input DNA HU 1

description: control after HU release

tag: cell line


title: H3S57ph_2 ChIP-Seq HU

description: ChIP-seq of H3S57ph from cells released from 2h HU treatment

value: H3S57ph (Fisher lab rabbit polyclonal)


title: input DNA control 1

description: control exponentially growing cells

value: control


title: WholeBlood_CRC305DGENT0073006_Day3


title: input DNA control 2

description: control exponentially growing cells


title: WholeBlood_CRC305DGENT1483036_Day3


title: H3S57ph_1 ChIP-Seq HU


title: H3S57ph_1 ChIP-Seq control

description: ChIP-seq of H3S57ph from exponentially growing cells


title: WholeBlood_CRC305DGENT0123021_Day7


title: WholeBlood_CRC305DGENT2211046_Day3


title: WholeBlood_CRC305DGENT2343042_Day7


title: WholeBlood_CRC305DGENT1831059_Day21


title: WholeBlood_CRC305DGENT1291026_Day0


title: WholeBlood_CRC305DGENT0141011_Day0


title: WholeBlood_CRC305DGENT0383009_Day3


title: WholeBlood_CRC305DGENT0191018_Day3


title: WholeBlood_CRC305DGENT0223019_Day7


title: WholeBlood_CRC305DGENT1351022_Day21


title: WholeBlood_CRC305DGENT0223019_Day1


title: WholeBlood_CRC305DGENT0041017_Day7


title: WholeBlood_CRC305DGENT0411008_Day21


title: WholeBlood_CRC305DGENT1281024_Day0


title: WholeBlood_CRC305DGENT2381052_Day21


title: H3S57ph_2 ChIP-Seq control


title: WholeBlood_CRC305DGENT2351058_Day3

value: other


title: WholeBlood_CRC305DGENT0361005_Day7


title: WholeBlood_CRC305DGENT1713056_Day21


title: RCC_urine_5hMethylCap-seq

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

description: pool.UA

data_processing:
library strategy:5hMethylCap-seq
The 5hMethylCap-Seq raw reads were trimmed for Illumina TruSeq adapters and low quality bases.  Trimmed and filtered fastq were mapped to hg19 reference genome using bowtie 1.1.2. Alignment will be converted to bam with SAMtools 1.3.1, and duplicate reads removed with picard v2.4.1. For peak calling, the 5hmC sample bam files were downsampled to 4 million reads.  The histone methylation regions were called using a Model-based Analysis of ChIP-Seq (MACS2) using the full Input sample as a control. Complete peak files are included for download.  For comparison purposes, peaks within 1 kb were merged with samples and across samples.
To determine the relationship between H3K9 and DNA methylation, we correlated the genome-wide 5mC/5hmC profiles with histone modification profiles from ChIP-Seq (DONOR_ID: 27, clear cell type), as well as with genomic features and data from the publicly available histone database (NIH Roadmap Epigenomics Mapping Consortium, JASPAR motif database and UCSC Genome Browser database). Average profile plots from sequencing reads of regions with differential 5hmC marks and histone modifications were generated using ngs.plot (version 2.0.8).  DiffBind was used for differential binding analysis of ChIP-seq peak data.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: NARROWPEAK files generated with MACS2 comparing each downsampled 5hmC sample to Input

growth_protocol: Human renal clear cell carcinoma cell lines VHL-WT Caki-1 and VHL-null Caki2 were purchased from the American Type Culture Collection (ATCC). The cells were passaged in RPM11640 medium with 10% FBS and 1% Penicillin Streptomycin. To systematically study the association between H3K9me3 and 5hmC in RCC cells, we established stable SUV39H1 knockdown VHL-WT Caki-1 cells and VHL-null Caki-2 cells using short hairpin RNA.

extract_protocol:
Tissue and cell line DNA were processed by DNeasy Blood & Tissue kit (Qiagen) according to manufacturer’s requirement. Total DNA was extracted from urine samples using ZR Urine DNA Isolation Kit (Zymo Research).
The DNA samples were sheared by sonication using the Covaris S220 (COVARIS, INC.) to achieve an averaged DNA fragment size around 300 bp. The immunoprecipitation was performed using the Methylated DNA Capture Kit (Diagenode) and the IP-Star Compact Automated System (Diagenode). The libraries were generated using PrepX ILM DNA Library Kit (Illumina) per manufacturer’s instructions. Library quantification is performed using Qubit (Invitrogen) and Labchip GX HS (PerkinElmer) system for library fragment analysis. The libraries were subjected to massively parallel sequencing using HiSeq 2500 (Illumina) platform with the single-end 50 bp read option, according to the manufacturer’s instructions.

tag: tissue source

value: urine

tag: tissue/cell type

value: clear cell renal cell carcinoma

tag: sample type

value: 5hmC (Diagenod, C02010033)


title: NAT_tissue_5hMethylCap-seq

description: pool.KBP

value: kidney

value: normal adjacent tissue

value: tissue


title: Caki2_shSUV39H1_5hMethylCap-seq

value: cell line

tag: genotype/variation


title: RCC_tissue_5hMethylCap-seq

description: pool.KAP


title: Normal_urine_5hMethylCap-seq

description: pool.UB

value: normal urine


title: WholeBlood_CRC305DGENT1883049_Day7

tag: participant

tag: gender

value: female

tag: age

value: FLUADD


title: Caki1_shSUV39H1_5hMethylCap-seq


title: CD46-KO/CD46-CYT1

city: Wuhan

first: Jin

last: Zeng

address: Jiefang Avenue

institute: Tongji Hospital

data_processing:
Raw data (raw reads) were processed using NGS QC Toolkit.
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference homo sapiens genome using bowtie2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq (2012) functions estimateSizeFactors and nbinomTest.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

source_name: human baldder carcinoma cell line EJ-1

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

value: human baldder carcinoma cell line


title: Caki1_shCTL_5hMethylCap-seq

value: shCTL


title: CD46-KO/CD46-CYT2


title: WholeBlood_CRC305DGENT0123021_Day0

tag: race

value: white

tag: ethnicity

tag: protocol

value: whole blood


title: WholeBlood_CRC305DGENT0333003_Day3

value: not american hispanic or latino

tag: treatment

tag: day

tag: tissue


title: WholeBlood_CRC305DGENT1803057_Day3


title: WholeBlood_CRC305DGENT0373010_Day3


title: WholeBlood_CRC305DGENT2193048_Day1


title: WholeBlood_CRC305DGENT1521035_Day0

value: male


title: WholeBlood_CRC305DGENT2211046_Day0


title: WholeBlood_CRC305DGENT1593031_Day0


title: CD46-KO/control vector

tag: cell type

value: control vector


title: WholeBlood_CRC305DGENT2351058_Day21

value: other


title: WholeBlood_CRC305DGENT1623033_Day7


title: Caki2_shCTL_5hMethylCap-seq

value: clear cell renal cell carcinoma


title: WholeBlood_CRC305DGENT1493038_Day3


title: WholeBlood_CRC305DGENT1803057_Day0


title: WholeBlood_CRC305DGENT1471032_Day21


title: WholeBlood_CRC305DGENT0191018_Day1


title: WholeBlood_CRC305DGENT2391057_Day0


title: WholeBlood_CRC305DGENT1593031_Day1


title: WholeBlood_CRC305DGENT0351013_Day0


title: WholeBlood_CRC305DGENT2423054_Day7


title: WholeBlood_CRC305DGENT2193048_Day3


title: WholeBlood_CRC305DGENT1883049_Day21


title: WholeBlood_CRC305DGENT0233014_Day7


title: SDf_T8h_H_205 HVC, biological rep 1

city: Seewiesen

first: Meng-Ching

last: Ko

state: Bayern

address: Eberhard-Gwinner-Str. 6a

department: Behavioral Neurobiology

institute: Max Planck Institute for Ornithology

description: HVC was dissected from cryosections

hyb_protocol: The resulting cDNA was hybridized to the Custom Affymetrix Gene Chip® MPIO-ZF1s520811 Exon Array. The hybridization was carried out during 16 hours at 45°C and 60 rpm in the GeneChip Hybridization Oven 640.

scan_protocol: The arrays were washed, stained and scanned using the Affymetrix GeneChip Fluidics Station 450 and Affymetrix GeneChip scanner 3000 7G.

data_processing:
The CEL files were generated by the Affymetrix® GeneChip® Command Console® Software (AGCC) and the quality control for evaluating the success of individual hybridizations was assessed by the Affymetrix® Expression Console™ software. Affymetrix CEL files were imported into ChipInspector software, version 21 (El Dorado Database version: vE28R1306 Genomatix GmbH (http://www.genomatix.de)
Quantile normalized gene level expression values calculated using the justRMA function of the affy R package. The normalized values were collapsed to transcript-level using the collapseRows function of the WGCNA R package.

organism: Taeniopygia guttata

source_name: HVC

label_protocol: RNA was processed for hybridization on the microarray by using the Ambion WT Expression Kit and the Affymetrix WT Terminal Labeling and Controls Kit.

growth_protocol: Adult animals housed in short light cycles 9/15 (light/dark) in aviaries. Water and food were available ad libidum.

extract_protocol: For RNA preparation, brains were cut into four 40 µm para-sagittal sections mounted each on one slide . The areas were dissected with very fine forceps (a different one for each brain area to avoid contamination) under a stereo-microscope, transferred into 340μl RLT buffer mixture (containing DTT, Qiagen) and stored at -80 C till RNA purification (RNeasy® Micro Kit, Qiagen).

treatment_protocol: A 7-mm SilasticTM tube filled with testosterone was placed subcutaneously over the pectoral musculature for intended periods (1h, 3h, 8h, 3d, 7d, and 14d)

value: adult

tag: Sex

tag: light cycle

value: short day:9/15 (light/dark)

tag: breeding

value: non-breeding

value: Testosterone implantation for 8 hour(s)

tag: song behavior

value: Non-singing


title: WholeBlood_CRC305DGENT0273001_Day3


title: WholeBlood_CRC305DGENT0351013_Day7


title: WholeBlood_CRC305DGENT1371020_Day1


title: WholeBlood_CRC305DGENT1851047_Day21

value: PLACEBOD


title: SDf_T8h_H_207 HVC, biological rep 3

description: HVC was dissected from cryosections

value: female


title: WholeBlood_CRC305DGENT2361060_Day21

value: FLUADD


title: WholeBlood_CRC305DGENT0241003_Day0


title: SDf_T8h_H_305L HVC, biological rep 5

description: HVC was dissected from cryosections


title: WholeBlood_CRC305DGENT0011001_Day3


title: SDf_T7d_H_793R HVC, biological rep 6

description: HVC was dissected from cryosections

value: Testosterone implantation for 7 day(s)

value: Singing


title: WholeBlood_CRC305DGENT1573034_Day1

value: white


title: SDf_T8h_H_208 HVC, biological rep 4

description: HVC was dissected from cryosections


title: WholeBlood_CRC305DGENT1461019_Day7

value: whole blood


title: WholeBlood_CRC305DGENT1361021_Day1

value: not american hispanic or latino


title: SDf_T8h_H_206 HVC, biological rep 2

description: HVC was dissected from cryosections


title: SDf_T7d_H_791R HVC, biological rep 4

description: HVC was dissected from cryosections


title: SDf_T7d_H_790R HVC, biological rep 3

description: HVC was dissected from cryosections


title: WholeBlood_CRC305DGENT0181014_Day0

value: male


title: WholeBlood_CRC305DGENT1603032_Day1


title: SDf_T7d_H_789R HVC, biological rep 2

description: HVC was dissected from cryosections


title: SDf_T3h_H_767R HVC, biological rep 4

description: HVC was dissected from cryosections

value: Testosterone implantation for 3 hour(s)


title: WholeBlood_CRC305DGENT1843044_Day3


title: WholeBlood_CRC305DGENT2303051_Day21


title: WholeBlood_CRC305DGENT1703047_Day0


title: WholeBlood_CRC305DGENT0393007_Day1


title: SDf_T3h_H_765R HVC, biological rep 3

description: HVC was dissected from cryosections


title: SDf_T3h_H_774L HVC, biological rep 5

description: HVC was dissected from cryosections


title: SDf_T3h_H_764R HVC, biological rep 2

description: HVC was dissected from cryosections


title: WholeBlood_CRC305DGENT2453055_Day1


title: WholeBlood_CRC305DGENT1803057_Day1


title: WholeBlood_CRC305DGENT1581031_Day3


title: WholeBlood_CRC305DGENT1503022_Day0


title: WholeBlood_CRC305DGENT2433059_Day21


title: SDf_T7d_H_792R HVC, biological rep 5

description: HVC was dissected from cryosections


title: SDf_T7d_H_788L HVC, biological rep 1

description: HVC was dissected from cryosections


title: SDf_T3h_H_755R HVC, biological rep 1

description: HVC was dissected from cryosections


title: WholeBlood_CRC305DGENT0361005_Day1


title: Adult_6

city: Rehovot

first: Jonathan

middle: Aryeh

last: Sobel

address: Benoziyo Building for Biological Sciences, room 277S, Weizmann Institute of Science

department: Biomolecular Sciences

country: Israel

institute: Weizmann Institute of science

description: ATAC-seq

data_processing:
Fastq files quality was assessed using FastQC (version 0.11.2).
Raw reads were aligned to the Rattus norvegicus reference genome assembly 5 (Rn5) using BWA (version 0.7.13) with default settings.
Quality control of the aligned reads was checked using Samstat (version 1.5) and processed with Samtools (version 1.3).
bigwig we produced using dnase_wig_tracks.py script from the pyDNase library and wigToBigwig script
Peak calling was performed in order to find accessible sites (ACSs) using Macs2 (version 2.1.1)with the folowing parameters:--nomodel --shift -100 --extsize 200. Peaks with a width below 200bp were discarded.
ACSs were then reunited in a single bed file and quantified using the pyDNase library (version 0.2.5) and annotated with the closest TSS using ChIPpeakanno package from R.
differential accesibility analysis was performed with the edge R package
Genome_build: Rn5
Supplementary_files_format_and_content: peak annotations/quantification and statistical analysis table (CSV)

organism: Rattus norvegicus

source_name: Pancreatic Islets

growth_protocol: male and female pups were nursed until sacrifice at P10. All procedures were performed in accordance with the Guide for the care and use of laboratory animals from the National Institutes of Health and were approved by the Swiss Research Councils and Veterinary Office.

extract_protocol:
3 mM EGTA and 0.002% trypsin for 5 min at 37°C.
Illumina). The transposition reaction was performed at 37°C for 30min and followed by the purification of the samples using the Qiagen MinElute PCR purification kit (Qiagen). Transposed DNA fragments were amplified for 11 cycles using the NEBnext high-fidelity PCR master mix and the Ad1_noMX and Ad2.1-2.6 barcoded primers from (Buenrostro 2013 Nat Method). Amplified libraries were purified with AMPure XP beads (Beckman Coulter) to remove contaminating primer dimers. Library quality was assessed using the Fragment Analyzer and quantitated using Qubit. All libraries were sequenced on Illumina HiSeq 2500 using 100 bp paired-end reads.

value: Adult


title: Adult_5

description: ATAC-seq


title: WholeBlood_CRC305DGENT1831059_Day1


title: Adult_4

description: ATAC-seq


title: SDf_T3d_H_248L HVC, biological rep 3

description: HVC was dissected from cryosections

value: Testosterone implantation for 3 day(s)


title: SDf_T3d_H_244L HVC, biological rep 1

description: HVC was dissected from cryosections

value: adult


title: SDf_T3d_H_302 HVC, biological rep 4

description: HVC was dissected from cryosections

value: short day:9/15 (light/dark)


title: SDf_T3d_H_414 HVC, biological rep 6

description: HVC was dissected from cryosections

value: non-breeding


title: WholeBlood_CRC305DGENT0403011_Day21


title: P10_3

description: ATAC-seq


title: SDf_T3d_H_413R HVC, biological rep 5

description: HVC was dissected from cryosections


title: WholeBlood_CRC305DGENT0283005_Day0


title: SDf_T1h_H_749R HVC, biological rep 5

description: HVC was dissected from cryosections

value: Testosterone implantation for 1 hour(s)


title: SDf_T3d_H_245L HVC, biological rep 2

description: HVC was dissected from cryosections

value: Non-singing


title: WholeBlood_CRC305DGENT2221043_Day1


title: WholeBlood_CRC305DGENT1221030_Day21


title: WholeBlood_CRC305DGENT1243023_Day0


title: WholeBlood_CRC305DGENT2303051_Day1


title: SDf_T1h_H_746L HVC, biological rep 4

description: HVC was dissected from cryosections


title: WholeBlood_CRC305DGENT0163013_Day0


title: WholeBlood_CRC305DGENT2331050_Day7


title: SDf_T1h_H_751L HVC, biological rep 6

description: HVC was dissected from cryosections


title: P10_1

description: ATAC-seq


title: P10_2

description: ATAC-seq


title: SDf_T14d_H_805R HVC, biological rep 6

description: HVC was dissected from cryosections

value: Testosterone implantation for 14 day(s)


title: SDf_T1h_H_743R HVC, biological rep 2

description: HVC was dissected from cryosections

value: female


title: SDf_T1h_H_741R HVC, biological rep 1

description: HVC was dissected from cryosections


title: SDf_T14d_H_804R HVC, biological rep 5

description: HVC was dissected from cryosections


title: SDf_T14d_H_803R HVC, biological rep 4

description: HVC was dissected from cryosections


title: SDf_T1h_H_745L HVC, biological rep 3

description: HVC was dissected from cryosections


title: SDf_T14d_H_799L HVC, biological rep 3

description: HVC was dissected from cryosections


title: WholeBlood_CRC305DGENT2391057_Day21

value: FLUADD


title: Sample of patient 19, sample al 8 weeks

city: Barcelona

first: Teresa

last: Torres Moral

address: Casanova, 143

country: Spain

institute: Universitat de Barcelona

description: Gene expression data from blood after 8 weeks of  Fluoxetine treatment

hyb_protocol: It was conducted using Affymetrix GeneTitan system (http://www.affymetrix.com/support/technical/byproduct.affx?product=genetitan), controlled by the Affymetrix GeneChip Command Console software v4.2 (http://www.affymetrix.com/support/technical/byproduct.affx?product=commandconsole) according to the manufacturer's instructions.

data_processing: Data processing was developed using Affymetrix GeneChip Expression Console v1.4 Software according to the manufacturer's instructions (https://www.thermofisher.com/es/es/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/affymetrix-expression-console-software.html).

label: Biotin

label_protocol: It was carried out as described in the Affymetrix GeneChip WT PLUS Reagent Kit User Manual according to the manufacturer's instructions  (https://www.thermofisher.com/order/catalog/product/902280).

extract_protocol:
Extraction from PAXgene blood RNA tubes of total RNA was performed according to the manufacturer's instructions (https://www.qiagen.com/us/shop/sample-technologies/rna/total-rna/paxgene-blood-rna-kit-ivd/#technicalspecification).
Purification of RNA sample was performed using RNeasy MinElute Cleanup Kit according to the manufacturer's instructions (https://www.qiagen.com/us/shop/sample-technologies/rna/rna-clean-up/rneasy-minelute-cleanup-kit/#orderinginformation).

value: Blood

tag: illness

value: Major Depressive Disorder


title: WholeBlood_CRC305DGENT1531041_Day7

value: white


title: WholeBlood_CRC305DGENT0283005_Day3

value: whole blood


title: WholeBlood_CRC305DGENT2351058_Day1

value: other

value: not american hispanic or latino


title: Sample of patient 20, sample al 8 weeks

scan_protocol: It was conducted using Affymetrix GeneTitan system (http://www.affymetrix.com/support/technical/byproduct.affx?product=genetitan), controlled by the Affymetrix GeneChip Command Console software v4.2 (http://www.affymetrix.com/support/technical/byproduct.affx?product=commandconsole) according to the manufacturer's instructions.


title: WholeBlood_CRC305DGENT1623033_Day21


title: WholeBlood_CRC305DGENT0063016_Day0


title: WholeBlood_CRC305DGENT1221030_Day7

value: male


title: Sample of patient 16, sample al 8 weeks


title: Sample of patient 11, sample al 8 weeks


title: WholeBlood_CRC305DGENT1691045_Day21


title: SDf_T14d_H_798L HVC, biological rep 2

description: HVC was dissected from cryosections

value: Singing


title: paps1-3_26 [small RNA]

city: Potsdam

first: Michael

last: Lenhard

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

data_processing:
RA3 adapters were removed using Trimmomatic (Bolger et al. 2014; doi:10.1093/bioinformatics/btu170).
The resulting reads were mapped against the Arabidopsis thaliana reference genome (TAIR10) using bwa (Li et al. 2009; doi:10.1093/bioinformatics/btp324) and further processed using samtools (Li et al. 2009; doi:10.1093/bioinformatics/btp352). Bam files were split by read length for 18 to 28 nucleotides using reformat.sh (https://sourceforge.net/projects/bbmap/).
Reads mapping to TAIR10 annotated gene exons and transposable elements (excluding overlaps with the prior ones) were counted using bedtools multicov (Quinlan and Hall 2010; doi:10.1093/bioinformatics/btq033).
Genome_build: TAIR10 (www.arabidopsis.org)
Supplementary_files_format_and_content: Raw read counts by length (18 to 28)

organism: Arabidopsis thaliana

extract_protocol:
Following the sorting of pollen grains, whole RNA was isolated using the Direct-Zol™ RNA MiniPrep Kit by Zymo Research (Irvine, California, US) since the specific columns provided in this kit prevent loss of small RNAs. The freshly sorted samples were centrifuged for 3 min at 3,000 rpm and the supernatant removed. Subsequently, the pollen were resuspended in 750 μl Tri-reagent LS (Sigma-Aldrich, St. Louis, US) and flash frozen in liquid nitrogen. The samples were ground in a cooled mortar to break up pollen grains until the samples liquefied and transferred to fresh reaction tubes. Afterwards, the protocol was followed according to the manufacturer’s specification. RNA concentration was measured using a NanoDrop and analysed on a BioAnalyzer to verify the existence of small RNAs as well as to check for possible RNA degradation.
Generation of small RNA libraries from three paired pollen RNA isolations (wild-type and paps1-3 mutant pollen sorted from the same sample) and sequencing was carried out by Eurofins Medigenomix GmbH, Ebersburg, Germany. Complementary DNA (cDNA) libraries were constructed containing fragments with a length of approximately 19-25 bp with TruSeqTM Small RNA Sample Preparation Kit (Illumina, San Diego, US) and sequencing was performed using Illumina HiSeq 2500.

tag: accession

value: Col

value: pollen


title: Sample of patient 15, sample al 8 weeks


title: WholeBlood_CRC305DGENT1371020_Day3


title: Sample of patient 17, sample al 8 weeks


title: SDf_CON_H_995L HVC, biological rep 5

description: HVC was dissected from cryosections

value: adult

value: short day:9/15 (light/dark)

value: Control bird implanted with empty tube


title: WholeBlood_CRC305DGENT1411039_Day21


title: SDf_T14d_H_797L HVC, biological rep 1

description: HVC was dissected from cryosections

value: non-breeding


title: WholeBlood_CRC305DGENT1321028_Day7


title: SDf_CON_H_982L HVC, biological rep 1

description: HVC was dissected from cryosections

value: Non-singing


title: Sample of patient 12, sample al 8 weeks

value: female


title: SDf_CON_H_986R HVC, biological rep 3

description: HVC was dissected from cryosections


title: Sample of patient 13, sample al 8 weeks


title: SDf_CON_H_992L HVC, biological rep 4

description: HVC was dissected from cryosections


title: Sample of patient 7, sample al 8 weeks


title: SDf_CON_H_984L HVC, biological rep 2

description: HVC was dissected from cryosections


title: Sample of patient 8, sample al 8 weeks


title: paps1-3_20 [small RNA]

tag: genotype/variation


title: WholeBlood_CRC305DGENT1211029_Day1

tag: participant

value: FLUADD


title: WholeBlood_CRC305DGENT1713056_Day7

tag: gender


title: Sample of patient 14, sample al 8 weeks

value: Blood

tag: age


title: Sample of patient 10, sample al 8 weeks

value: Major Depressive Disorder


title: WholeBlood_CRC305DGENT0383009_Day0

tag: race

value: white


title: WholeBlood_CRC305DGENT1393025_Day7

tag: ethnicity

value: PLACEBOD

value: whole blood


title: Sample of patient 6, sample al 8 weeks


title: Sample of patient 9, sample al 8 weeks


title: WholeBlood_CRC305DGENT1453037_Day0

value: not american hispanic or latino

tag: protocol


title: paps1-3_16 [small RNA]


title: WT_25 [small RNA]

source_name: wild type_pollen

value: wild type


title: WT_19 [small RNA]


title: WT_15 [small RNA]


title: WholeBlood_CRC305DGENT1461019_Day21

value: male

tag: treatment


title: WholeBlood_CRC305DGENT1503022_Day21

tag: day


title: iPSC-S (NC-iSN2)

city: Bethesda

first: Minh

middle: Q

last: Nguyen

state: MARYLAND

address: 9000, Rockville Pike

institute: NIDCR/NIH

data_processing:
bcl2fastq (v2.17) was used for basecalling
Sequence reads from 10x libraries were processed using Cell Ranger 2.1.0 from 10x Genomics (https://www.10xgenomics.com/)
Reads were aligned using STAR (v 2.5.3a) to GRCh38.v25.premRNA-2.1.0 genome.
Seurat package (v3) was used for downstream data analysis in R as described by the Satija lab (http://satijalab.org/seurat/)
Genome_build: GRCh38.v25.premRNA-2.1.0
Supplementary_files_format_and_content: csv files with cell barcodes and corresponding gene expression counts; only nuclei meeting minimum threshold of transcripts are included for analysis

source_name: Induced pluripotent stem cells

growth_protocol: Sensory neurons were differentiated from induced pluripotent stem cells (iPSCs) through a neural crest intermediate, using a well-characterized protocol (Schrenk-Siemens et al., Nat. Neuro., 2015). Neural crest cells were plated at 50,000 cells/cm2 on PEI/laminin-coated dishes and differentiated in a neural induction medium for 21 days before RNA extraction.

extract_protocol:
iPS cells were washed with ice cold PBS, lysed with EZ prep buffer (Sigma).  Nuclei were then washed with PBS and stained with trypan blue for counting using a hemocytometer.
Libraries construction were performed with method from 10x Genomics for 10x Chromium runs.

treatment_protocol: Neural crest cells in the NC-iSN1 condition were treated with doxycycline from day 0 of plating until day 14, and neurotrophic factors were supplemented beginning on day 8. For the NC-iSN2 condition, doxycycline was added on day 0 for 24 hours, and neurotrophic factors and retinoic acid were supplemented from day 0 onwards.

value: iPSC-derived sensory neuron


title: iPSC-L (NC-iSN1)


title: Sample of patient 4, basal sample

description: Gene expression data from blood previous to Fluoxetine treatment

tag: tissue


title: Sample of patient 2, sample al 8 weeks


title: Sample of patient 20, basal sample


title: Sample of patient 17, basal sample


title: WholeBlood_CRC305DGENT2401055_Day7


title: Sample of patient 13, basal sample


title: Sample of patient 15, basal sample


title: WholeBlood_CRC305DGENT0163013_Day3


title: Sample of patient 5, sample al 8 weeks


title: WholeBlood_CRC305DGENT1623033_Day0


title: Sample of patient 16, basal sample


title: WholeBlood_CRC305DGENT2371051_Day3


title: WholeBlood_CRC305DGENT2273043_Day0


title: WholeBlood_CRC305DGENT0073006_Day7


title: Sample of patient 8, basal sample


title: Sample of patient 10, basal sample


title: Sample of patient 14, basal sample


title: WholeBlood_CRC305DGENT2381052_Day7


title: Sample of patient 9, basal sample


title: WholeBlood_CRC305DGENT0241003_Day21


title: WholeBlood_CRC305DGENT0111015_Day0


title: Sample of patient 12, basal sample


title: WholeBlood_CRC305DGENT0411008_Day7


title: WholeBlood_CRC305DGENT1611036_Day1


title: Sample of patient 7, basal sample


title: WholeBlood_CRC305DGENT0111015_Day3


title: WholeBlood_CRC305DGENT0333003_Day1


title: WholeBlood_CRC305DGENT2203041_Day1


title: WholeBlood_CRC305DGENT1351022_Day0


title: mock_clone2 [miRNA]

city: Chiba

first: Ryosuke

last: Muroyama

address: Inohana 1-8-1, Chuo-ku

department: Department of Gastroenterology

country: Japan

institute: Graduate School of Medicine, Chiba University

description: Gene expression in mock cells

hyb_protocol: Samples were hybridized to array slides according to the manufacturer's protocol.

scan_protocol: The array slides were scanned with the Agilent SureScan Microarray Scanner.

data_processing: Scanned images were extracted and initial quality control performed using ImaGene 9 Software, and thr microarray data were normalized using the quantile method.

source_name: mock cells

label_protocol: 250 ng of total RNA was labeled with Hy3-dye using miRCURY LNATM microRNA Hi-Power Labeling Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: The fusion HBx in Hep3B cells was stably knockdowned by RNAi technique.

tag: cell line

value: Hep3B cells


title: Sample of patient 6, basal sample

tag: Sex


title: human brain Conrol

city: Fulda

first: Daniela

last: Fussbroich

address: Leipziger Str. 123

institute: University of Applied Sciences Fulda

data_processing:
PhiX Sequencing Control v3 and the MiSeq™ Desktop Sequencer (all Illumina Inc., San Diego, USA) for Base Calling
Results were processed according to Bioo Scientific Small RNA analysis pipeline.
Cutadapt V1.14 was used to remove adapter sequences and random bases and to discard too short reads
bowtie 2 (V2.2.9; http://www.bowtie-bio.sourceforge.net) was used to align readouts to murine mature miRNAs from miRBase (mature.fs, v21, June 2014; http://www.mirbase.org)
miRUtils (v1.0.0; http://www.mirutils.sourceforge.net) was used to process the aligned files
Genome_build: Mus musculus GRCm38 (v21)
Supplementary_files_format_and_content: coverage files including total reads per mapped miRNA

source_name: Brain

growth_protocol: Mice were purchased at the age of 6-8 weeks.

extract_protocol:
Lungs were removed, stored immediately in RNA later, and RNA was harvested using miRNeasy Mini Kit.
RNA libraries were prepared with 1 ug of total RNA for sequencing using standard NEXTflex Small RNA-Seq Kit v3.

treatment_protocol: Mice were first sensitized for 10 consecutive days with 40 µg house dust mite extract to induce allergic asthma and thereafter supplemented with the LCPUFA combination for 24 days. Within the last 3 days, mice daily received repetitive doses of HDM (recall).

value: Brain


title: Sample of patient 2, basal sample


title: Sample of patient 3, sample al 8 weeks


title: Sample of patient 3, basal sample


title: kd_clone2 [miRNA]

description: Gene expression in fusion HBx-knockdowned cells

source_name: kd cells


title: mock_clone1 [miRNA]

description: Gene expression in mock cells


title: kd_clone1 [miRNA]


title: WholeBlood_CRC305DGENT2401055_Day21

city: London

first: David

last: Lewis

address: Du Cane Road

institute: Imperial College London

data_processing: The scanned microarray images were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.

source_name: Peripheral Blood, PaxGene

extract_protocol: mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer


title: WholeBlood_CRC305DGENT1683046_Day1


title: WholeBlood_CRC305DGENT1301023_Day1


title: kd_clone1

data_processing: The scanned images were extracted and initial quality control performed using Agilent Feature Extraction Software, and the microarray data were normalized using the quantile method.

label_protocol: 100 ng of total RNA was converted into Cy3-dye labeled cRNA using One-Color Microarray-Based Gene Expression Microarray Analysis (Low Input Quick Amp Labeling) version 6.6 according to the manufacturer's instructions.

tag: clone number


title: WholeBlood_CRC305DGENT1233028_Day21


title: WholeBlood_CRC305DGENT1631034_Day7


title: WholeBlood_CRC305DGENT0421004_Day7


title: Sample 13_2MonF

city: New York

first: Yejing

last: Ge

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Sample 1-8: 50-bp sequences were aligned to mm10 using STAR and Gencode release M9 and counts generated from STAR output --quantMode GeneCounts; Sample 9-12: mapping was performed using Bowtie package with the parameters ‘‘–X 2000’’ and ‘‘–m 1’’ to align 50-bp paired-end reads; Sample 13-14: maping was performed using CellRanger package from 10x genomics
Genome_build: mm10
Supplementary_files_format_and_content: Sample 1-8: tab delimited, gene counts; Sample 9-12: bed files, ATAC peaks; Sample 13-14:  tab delimited, gene names, cells and counts, gene matrix

organism: Mus musculus

growth_protocol: Aged (24-month-old) or Young (2-month-old) C57B6 females backskin

extract_protocol:
Sample 1-8: Total RNA extracted via Trizol/Zymo RNA extraction kit; Sample 9-14: fresh single cell resuspension obtained from FACS sorting
Sample 1-8: Illumina TruSeq RNA Sample Preparation; Sample 9-12: tagmentation reactions with TnD transposase; Sample 13-14: GemCode Single-Cell Instrument and Single Cell 3’ Library & Gel Bead Kit v2 and Chip Kit (10x Genomics) according to the manufacturer’s protocol, and captured 4000 cells each sample
Sample 1-12: Pair end sequencing using 51 Cycles; Sample 13-14: Pair end sequencing using 75 Cycles (for 10x genomics) I1: Sample index read (i7 Illumina index), R1: Read 1 –barcode and UMI, R2: Read 2—biological reads)

treatment_protocol: Trypsin digested mouse backskin, FACS purified based on sort markers indicated

tag: strain

value: young (2-month-old)

value: Skin

tag: cell type

value: young skin epithelium

tag: sort markers

value: Lineage Neg, IntA6+


title: mock_clone2

description: Gene expression in mock cells


title: Sample 12_epi_young

value: female

value: young skin epidermal stem cells

value: Lineage Neg, IntA6Hi, CD34-Sca1+


title: WholeBlood_CRC305DGENT2343042_Day3

value: FLUADD


title: Sample 11_bu_young

value: young skin hair follicle stem cells

value: Lineage Neg, IntA6Hi, CD34+Sca1-


title: Sample 14_24MonF

value: aged (24-month-old)

value: aged skin epithelium


title: Sample 9_bu_old

value: aged skin hair follicle stem cells


title: WholeBlood_CRC305DGENT1511040_Day3

value: male

value: white

value: not american hispanic or latino

value: PLACEBOD

value: whole blood


title: mock_clone1

description: Gene expression in mock cells

value: Hep3B cells


title: Sample 8_YgEpd

source_name: YgEpd

value: young (2-month-old)

value: Skin


title: WholeBlood_CRC305DGENT1773058_Day1

value: female


title: Sample 7_YgEpd

value: young skin epidermal stem cells


title: kd_clone2


title: WholeBlood_CRC305DGENT2343042_Day0


title: WholeBlood_CRC305DGENT2291044_Day7


title: Sample 6_YgBu

source_name: YgBu


title: Sample 4_OdEpd

source_name: OdEpd

value: aged skin epidermal stem cells

value: Lineage Neg, IntA6Hi, CD34-Sca1+


title: Sample 5_YgBu

value: young skin hair follicle stem cells


title: Sample 10_epi_old


title: WholeBlood_CRC305DGENT1851047_Day0


title: Sample 3_OdEpd


title: Sample 2_OdBu

source_name: OdBu

value: Lineage Neg, IntA6Hi, CD34+Sca1-


title: Sample 1_OdBu

value: aged (24-month-old)


title: WholeBlood_CRC305DGENT1371020_Day21

value: FLUADD


title: WholeBlood_CRC305DGENT1691045_Day0


title: WholeBlood_CRC305DGENT2303051_Day0


title: JZ112

city: Shanghai

first: Yun

last: Liu

address: 130 Dong An Road

institute: Fudan University

data_processing:
RNA-seq data was aligned to mm10 genome using osa version 2.1.14 with default parameter
the gene counts were generated using htseq tool
differential expression genes were identified by deseq2 package
WGBS data was aligned to mm10 genome using Bsmooth pipeline to get depth of each CpG sites
differential methylated regions were identified using bsseq package
Genome_build: mm10
Supplementary_files_format_and_content: gene counts and CpG depth file were plain text formated
Supplementary_files_format_and_content: 1st column is the chromosome NO.
Supplementary_files_format_and_content: 2nd column is the coordinate of CpG cite on the chromosome (1-based)
Supplementary_files_format_and_content: 3rd column is the base type, i.e., if the base is C , the base type is 1 , G then 4. (the binucleotide arrangement is CG)
Supplementary_files_format_and_content: we average the CpG methylation profile on both the forward and backward strand by this trick.
Supplementary_files_format_and_content: 4th column is the number of methylated C at this CpG site
Supplementary_files_format_and_content: 5th column is the total number of CpG site

extract_protocol:
After the middle cerebral artery occlusion, animal brains were removed, and the ipsilateral (IPC treatment) and contralateral cortices (serve as control) of the same brain were collected. Total RNA was isolated from three mouse brains using Trizol reagent. A total of two micrograms of RNA per sample was used as input material for library construction. Genomic DNA was isolated from three mouse brains using a DNeasy Blood & Tissue Kit according to the manufacturer’s instructions. A total of 500 ng of DNA spiked with 5 ng of lambda DNA (Promega, Madison, WI) per sample was used as input material for library construction.
Ribosomal RNA (rRNA) was removed by an Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA) according to the manufacturer’s instructions. Subsequently, strand-specific sequencing libraries were generated with the dUTP method using the resulting RNA by an NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations. For WGBS, a total of 500 ng of DNA spiked with 5 ng of lambda DNA (Promega, Madison, WI) per sample was fragmented to 250-350 bp by sonication with a Covaris M220, followed by end repair and methylated adaptor ligation. These DNA fragments were treated with bisulfite using an EZ DNA Methylation-Gold TM Kit. The obtained single-strand DNA fragments were amplified by PCR using KAPA HiFi HotStart Uracil + ReadyMix (2x) followed by purification by AMPure XP magnetic beads. The library concentration was quantified by a Qubit 2.0 Fluorometer, and the insert size was assessed on an Agilent Bioanalyzer 2100 system.
RNA-Seq, WGBS

value: brain

value: 8 weeks

value: left hemisphere of experimental stroke model (Control)


title: WholeBlood_CRC305DGENT0251006_Day21

value: male

value: white

value: not american hispanic or latino


title: JZ113


title: WholeBlood_CRC305DGENT0191018_Day21

value: whole blood


title: WholeBlood_CRC305DGENT1361021_Day21


title: WholeBlood_CRC305DGENT2441054_Day3


title: WholeBlood_CRC305DGENT0333003_Day7


title: WholeBlood_CRC305DGENT1573034_Day0


title: WholeBlood_CRC305DGENT2423054_Day21


title: JZ110


title: JZ109

value: right hemisphere of experimental stroke model (IPC treatment)


title: JZ108


title: WholeBlood_CRC305DGENT2291044_Day21


title: WholeBlood_CRC305DGENT1603032_Day7

value: PLACEBOD


title: 1012L


title: WholeBlood_CRC305DGENT2413052_Day7

value: female


title: 1011L


title: 1009L


title: 1012R


title: WholeBlood_CRC305DGENT2321056_Day0


title: WholeBlood_CRC305DGENT0291007_Day3


title: 1011R


title: WholeBlood_CRC305DGENT1593031_Day3


title: 1009R


title: WholeBlood_CRC305DGENT2401055_Day0


title: WholeBlood_CRC305DGENT1361021_Day3


title: WholeBlood_CRC305DGENT1653039_Day3


title: JZ107


title: WholeBlood_CRC305DGENT0103017_Day1


title: WholeBlood_CRC305DGENT2203041_Day21


title: WholeBlood_CRC305DGENT2221043_Day0


title: WholeBlood_CRC305DGENT2193048_Day0


title: WholeBlood_CRC305DGENT1503022_Day7


title: WholeBlood_CRC305DGENT2321056_Day1


title: WholeBlood_CRC305DGENT0343002_Day1


title: WholeBlood_CRC305DGENT1713056_Day1


title: WholeBlood_CRC305DGENT1453037_Day3


title: WholeBlood_CRC305DGENT0321012_Day0


title: WholeBlood_CRC305DGENT0203018_Day7


title: WholeBlood_CRC305DGENT2273043_Day1


title: WholeBlood_CRC305DGENT0063016_Day7


title: PC3_OVnc_rep2

first: Xiaolei

address: 168 Changhai Road

department: Department of Urology

institute: Shanghai Changhai Hospital

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 9 out of 18 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: PC3 human prostate cancer cells, overexpression negative control, replicate 2

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: PC3 was cultured with F-12 medium (GIBCO) supplemented with 10% fetal bovine serum, incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to the manufacture’s protocol. Reverse transcription was performed using ReverTra Ace RT Kit (TOYOBO, Japan). RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PC3 cells was transfected with lentiviruses of lncAPP-OV and lncAPP-shRNA.

value: overexpression  of lncAPP

value: prostate


title: WholeBlood_CRC305DGENT1461019_Day1


title: PC3_OVnc_rep3

source_name: PC3 human prostate cancer cells, overexpression negative control, replicate 3


title: WholeBlood_CRC305DGENT0203018_Day1


title: WholeBlood_CRC305DGENT0241003_Day3


title: PC3_OVlnc_rep2

source_name: PC3 human prostate cancer cells, overexpression lnc, replicate 2


title: WholeBlood_CRC305DGENT2291044_Day3


title: PC3_OVnc_rep1

source_name: PC3 human prostate cancer cells, overexpression negative control, replicate 1


title: PC3_OVlnc_rep3

source_name: PC3 human prostate cancer cells, overexpression lnc, replicate 3


title: WholeBlood_CRC305DGENT1271037_Day7


title: WholeBlood_CRC305DGENT1803057_Day21