title: Jingpo from Huyu, Ruili, Yunnan, China D2

description:
JYHRD2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo5-6h_E2_H7

status: Public on Dec 31 2019

type: SRA

city: Basel

first: Jialin

last: Liu

address: biozentrum, Spitalstrasse 41

country: Switzerland

institute: University of Basel

library_source: transcriptomic

data_processing:
Libraries were sequenced on an Illumina Hi-Seq 2500 with pair-end protocol.
The fastq files were first de-multiplexed by using the “Demultiplex” tool from BRB-seqTools suite (available at https://github.com/DeplanckeLab/BRB-seqTools).
Then, we trimmed the polyA sequences of the de-multiplexed files by using the “Trim” tool.
Next, the STAR aligner (Dobin et al. 2013) was used to map the trimmed reads to the reference genome of fly (BDGP6, Ensembl release 91 )
Genome_build: BDGP6
Supplementary_files_format_and_content: tabular expression matrix, read counts

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: single embryo

growth_protocol: Fly reared at room temperature on a standard fly medium with 12 hours light dark cycle.

extract_protocol:
For RNA extraction, tubes were thawed on ice, supplemented with 350 µL of 100% Ethanol before homogenizing again with the same parameters. We then used the Direct-zol™ RNA Miniprep R2056 Kit, with the following modifications: we did not perform DNAse I treatment, we added another 2 min centrifugation into an empty column after the RNA Wash step, finally elution was performed by adding 8 µL of RNAse-free water to the column, incubation at room temperature for 2 min and then centrifugation for 2 min. RNA was transferred to a low-binding 96 well plate and stored at -80°C.
RNA quantity was assessed using picogreen (Invitrogen P11496). Samples were then grouped according to their concentration in 96-well plates, and diluted to a final concentration determined by the lowest sample concentration on the plate. RNA was then used for gene expression profiling using BRB-seq. In short, the BRB-seq protocol starts with oligo-dT barcoding, without TSO for the first-strand synthesis (reverse transcription), performed on each sample separately. Then all samples are pooled together, after which the second-strand is synthesized using DNA PolII Nick translation. The sequencing library is then prepared using cDNA augmented by an in-house produced Tn5 transposase preloaded with the same adapters (Tn5-B/B), and further enriched by limited-cycle PCR with Illumina compatible adapters. Libraries are then size-selected (200 - 1000 bp), profiled using High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, #DNF-474), and measured using Qubit dsDNA HS Assay Kit (Invitrogen, #Q32851).

treatment_protocol: Eggs were harvested using the following protocol. First a 1:1 bleach (Reactolab 99412) 1x PBS mix was poured on the plate and incubated for 2 min. During this incubation, we used a brush to lightly scrape the surface to mobilize the embryos. We then poured the PBS-bleach mixture through a sieve, washed the plate with 1x PBS, and poured the wash on the same sieve. We washed the sieve several time with 1x PBS until the smell of bleach disappeared. Single embryos were then manually transferred to Eppendorf containing 50 µL beads and 350 µL Trizol (lifetechnologies AM9738). The tubes were homogenized in a Precellys 24 Tissue Homogenizer at 6000 rpm for 30 seconds. Samples were then transferred to liquid nitrogen for flash freezing and stored at –80°C.

tag: strain

tag: development stage

value: 5-6 hours

tag: tissue

value: whole embryo


title: Jingpo from Huyu, Ruili, Yunnan, China F1

type: genomic

city: Kunming

first: Ya-ping

last: Zhang

state: Yunnan

address: 32 Jiaochang Donglu

department: State Key Laboratory of Genetic Resources and Evolution

country: China

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

description:
JYHRF1
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48oC, single-base extension and allele-specific staining was performed according to the manufacturer's protocols.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 50-55 min at 0.68 bar and scanned on iScan system.

data_processing:
Genomic DNA extracted from whole blood was genotyped using Infinium Human OmniZhongHua-8 Genotyping BeadChips (Illumina).
1. kizwangwz-geo_matrix.xy.txt.gz: the genotype matrix file for chromosome X and Y.   2. kizwangwz-geo_matrix.txt.gz: the genotype matrix file for autosomal chromosomes.
Genotype: AA,AB,BB,or NC (no call)

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37oC using multi-sample amplification mixs 1 and 2 (MA1 and MA2) and multi-sample amplification master mix (MSM). After incubation the amplified DNA was fragmented with fragmentation solution (FMS), precipitated with precipitation solution (PM1) and isopropanol and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from whole blood was performed using QIAmp DNA Blood Mini Kit (Qiagen) according to the manufacturer’s protocols.

tag: gender

value: Male

tag: ethnic group

value: Jingpo

tag: location

value: Huyu, Ruili, Yunnan, China


title: Rakhine from Satthwa, Thandwe, Rakhine, Myanmar 842

description:
RRS842
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Rakhine

value: Satthwa, Thandwe, Rakhine, Myanmar


title: unexposed, biological rep3

type: RNA

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

country: USA

institute: SUNY-University at Albany

description: U-87 MG unexposed control cells

hyb_protocol: labeled samples were hybridized to Human Gene 2.0  ST Array (Affymetrix) using standard protocol

scan_protocol: The arrays were scanned on a GCS3000 7G scanner using standard Affymetrix protocols

data_processing: The CEL files were converted to CHP files using RMA in Expression Console 3.0 and used for statistical analysis (ANOVAp<0.05) in Transcriptome Analysis Console 3.0

label: biotin

molecule: total RNA

source_name: U-87 MG unexposed control cells

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

growth_protocol: U-87 MG cells were plated at a density of 4x10^5 cells/100-mm dish in Minimum Essential Medium with Earle’s salts and non-essential amino acids (Gibco/Life Technologies, Grand Island, NY) containing 10% fetal bovine serum (FBS) (Atlanta Biologicals, Norcross, GA) and 1mM sodium pyruvate (Gibco) in a humidified 5% CO2 incubator at 37°C.

extract_protocol: total RNA was isolated using RNEasy protocol with an on column DNase step. The RNA was checked for quality using a nanodrop and a bioanalyzer nanochip (Agilent).

treatment_protocol: 24 h after seeding, the plates were randomized to the treatment culture box inside the Faraday chamber and exposed continuously for 54 h to  RGFIELDS™ targeting four specific molecules [hsa-miRNA-381; mutated alpha-kinase 2 gene; HSP70 (70 kDa heat shock protein); CHI3L1 (chitinase-3-like protein 1)], or to the control culture box outside the Faraday chamber, to serve as the unexposed controls.  The culture boxes contained a continuous supply of 5% CO2/95% air mixture at 37°C.

tag: cell line

value: U-87 MG

value: glioblastoma cells


title: Rakhine from Satthwa, Thandwe, Rakhine, Myanmar 844

description:
RRS844
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Yebawgyi, Thandwe, Rakhine, Myanmar 848

description:
RRY848
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Yebawgyi, Thandwe, Rakhine, Myanmar


title: embryo5-6h_E2_A3


title: embryo5-6h_E3_D1


title: Rakhine from Satthwa, Thandwe, Rakhine, Myanmar 840

description:
RRS840
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Satthwa, Thandwe, Rakhine, Myanmar 837

description:
RRS837
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Female


title: Rakhine from Satthwa, Thandwe, Rakhine, Myanmar 836

description:
RRS836
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Satthwa, Thandwe, Rakhine, Myanmar 832

description:
RRS832
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Kyaukkyi, Thandwe, Rakhine, Myanmar 831

description:
RRG831
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Kyaukkyi, Thandwe, Rakhine, Myanmar


title: Rakhine from Kyaukkyi, Thandwe, Rakhine, Myanmar 827

description:
RRG827
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Kyaukkyi, Thandwe, Rakhine, Myanmar 823

description:
RRG823
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: BT474 sensitive, non-treated, n2

city: Madrid

first: Juan

last: Madoz-Gúrpide

state: Madrid

address: Avda. Reyes Católicos, 2

department: Anatomical Pathology

country: Spain

institute: Health Research Institute Fundación Jiménez Díaz

hyb_protocol: Hybridized to Human Exon 1.0 ST Array for 16h at 45ºC in a GeneChip Hybridization Oven 640

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Raw data was normalized by the RMA method using the oligo package (available at Bioconductor). Probes were mapped to gene ids using the hugene20sttranscriptcluster.db package (available at Bioconductor). The normalized expression value of multiple probes mapped to the same gene was merged taken the average value.

source_name: breast cancer cell line BT-474

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix)

growth_protocol: BT-474 cells were maintained in DMEM-F12 supplemented with 10% heat-inactivated fetal bovine serum (FBS), 2 mmol/L glutamine, and 1% penicillin G-streptomycin.

extract_protocol: RNeasy mini Kit (Qiagen)

treatment_protocol: The trastuzumab-conditioned BT-474.R cell lines were established by culturing the BT-474 cell line in the appropriate media supplemented with 15 μg/ml of recombinant humanized monoclonal HER2 antibody, trastuzumab (Herceptin, Genentech, USA). Trastuzumab was dissolved in sterile water at a stock concentration of 20 mg/ml. Resistant populations were obtained for the four cell lines through lifetime exposure to the drug for a minimum of 8 months.


title: embryo5-6h_E2_B8


title: embryo5-6h_E2_G4


title: embryo5-6h_E2_A11


title: embryo5-6h_E2_B3


title: embryo5-6h_E2_F10


title: embryo5-6h_E2_D9


title: embryo5-6h_E2_H8


title: embryo5-6h_E2_A9


title: embryo5-6h_E2_A4


title: embryo5-6h_E2_A7


title: embryo5-6h_E2_D7


title: embryo5-6h_E2_B7


title: embryo5-6h_E1_2_H7


title: embryo5-6h_E2_G9


title: embryo5-6h_E1_2_E6


title: embryo5-6h_E1_2_G11


title: embryo5-6h_E1_1_C10


title: embryo5-6h_E1_2_E2


title: embryo5-6h_E1_1_B10


title: embryo2-3h_E3_F11

value: 2-3 hours


title: embryo5-6h_E1_1_D10


title: embryo5-6h_E1_1_D9


title: embryo5-6h_E1_1_B7


title: embryo2-3h_E3_G4


title: Rakhine from Kyaukkyi, Thandwe, Rakhine, Myanmar 818

description:
RRG818
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Kyaukkyi, Thandwe, Rakhine, Myanmar 817

description:
RRG817
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo2-3h_E3_H9


title: embryo2-3h_E3_A8


title: embryo2-3h_E3_B2


title: embryo2-3h_E3_F5


title: embryo2-3h_E3_A7


title: Rakhine from Kyaukkyi, Thandwe, Rakhine, Myanmar 815

description:
RRG815
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Kyaukkyi, Thandwe, Rakhine, Myanmar 816

description:
RRG816
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo2-3h_E3_G12


title: Bamar from Yegyi, Pathein, Ayeyarwady, Myanmar 789

description:
BAY789
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Bamar

value: Yegyi, Pathein, Ayeyarwady, Myanmar


title: Bamar from Yegyi, Pathein, Ayeyarwady, Myanmar 791

description:
BAY791
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Kyeintali, Thandwe, Rakhine, Myanmar 804

description:
RRK804
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Kyeintali, Thandwe, Rakhine, Myanmar


title: Rakhine from Kyeintali, Thandwe, Rakhine, Myanmar 798

description:
RRK798
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Kyeintali, Thandwe, Rakhine, Myanmar 794

description:
RRK794
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Kyeintali, Thandwe, Rakhine, Myanmar 799

description:
RRK799
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Kyeintali, Thandwe, Rakhine, Myanmar 809

description:
RRK809
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Kyeintali, Thandwe, Rakhine, Myanmar 808

description:
RRK808
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Kyeintali, Thandwe, Rakhine, Myanmar 793

description:
RRK793
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Kyeintali, Thandwe, Rakhine, Myanmar 801

description:
RRK801
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo2-3h_E3_C8


title: embryo2-3h_E3_D3


title: embryo2-3h_E3_A10


title: embryo2-3h_E3_C1


title: embryo2-3h_E3_F4


title: embryo2-3h_E3_A12


title: BT474 resistant, non-treated, n1


title: embryo2-3h_E2_C12


title: embryo2-3h_E3_C9


title: embryo2-3h_E2_E1


title: embryo2-3h_E2_H11


title: Bamar from Yegyi, Pathein, Ayeyarwady, Myanmar 780

description:
BAY780
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kyangin, Hinthada, Ayeyarwady, Myanmar 756

description:
BAK756
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Kyangin, Hinthada, Ayeyarwady, Myanmar


title: Bamar from Hinthada, Hinthada, Ayeyarwady, Myanmar 761

description:
BAH761
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Hinthada, Hinthada, Ayeyarwady, Myanmar


title: Bamar from Hinthada, Hinthada, Ayeyarwady, Myanmar 768

description:
BAH768
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Hinthada, Hinthada, Ayeyarwady, Myanmar 767

description:
BAH767
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Yegyi, Pathein, Ayeyarwady, Myanmar 787

description:
BAY787
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Yegyi, Pathein, Ayeyarwady, Myanmar 781

description:
BAY781
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Hinthada, Hinthada, Ayeyarwady, Myanmar 771

description:
BAH771
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Hinthada, Hinthada, Ayeyarwady, Myanmar 766

description:
BAH766
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Hinthada, Hinthada, Ayeyarwady, Myanmar 759

description:
BAH759
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Yegyi, Pathein, Ayeyarwady, Myanmar 774

description:
BAY774
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Yegyi, Pathein, Ayeyarwady, Myanmar 775

description:
BAY775
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Yegyi, Pathein, Ayeyarwady, Myanmar 783

description:
BAY783
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo2-3h_E2_D2

value: whole embryo


title: Bamar from Kyangin, Hinthada, Ayeyarwady, Myanmar 749

description:
BAK749
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Male


title: Bamar from Kyangin, Hinthada, Ayeyarwady, Myanmar 751

description:
BAK751
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kyangin, Hinthada, Ayeyarwady, Myanmar 747

description:
BAK747
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kyangin, Hinthada, Ayeyarwady, Myanmar 742

description:
BAK742
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kyangin, Hinthada, Ayeyarwady, Myanmar 739

description:
BAK739
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kyangin, Hinthada, Ayeyarwady, Myanmar 738

description:
BAK738
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Shwedaung, Pyay, Bago, Myanmar 735

description:
BBS735
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Shwedaung, Pyay, Bago, Myanmar


title: Bamar from Shwedaung, Pyay, Bago, Myanmar 733

description:
BBS733
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo2-3h_E2_E10


title: BT474 resistant, trastuzumab-treated, n1


title: Bamar from Shwedaung, Pyay, Bago, Myanmar 730

description:
BBS730
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: BT474 resistant, non-treated, n2


title: Bamar from Shwedaung, Pyay, Bago, Myanmar 729

description:
BBS729
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: BT474 resistant, trastuzumab-treated, n2


title: Bamar from Gyobingauk, Tharrawaddy, Bago, Myanmar 713

description:
BBG713
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Gyobingauk, Tharrawaddy, Bago, Myanmar


title: Bamar from Gyobingauk, Tharrawaddy, Bago, Myanmar 712

description:
BBG712
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo2-3h_E2_B6


title: Bamar from Gyobingauk, Tharrawaddy, Bago, Myanmar 718

description:
BBG718
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Shwedaung, Pyay, Bago, Myanmar 726

description:
BBS726
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Gyobingauk, Tharrawaddy, Bago, Myanmar 708

description:
BBG708
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Gyobingauk, Tharrawaddy, Bago, Myanmar 714

description:
BBG714
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo2-3h_E2_D6


title: embryo2-3h_E1_2_H8


title: Bamar from Shwedaung, Pyay, Bago, Myanmar 724

description:
BBS724
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Shwedaung, Pyay, Bago, Myanmar 721

description:
BBS721
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo2-3h_E2_E11


title: embryo2-3h_E1_2_H11


title: Bamar from Shwedaung, Pyay, Bago, Myanmar 719

description:
BBS719
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Letpadan, Tharrawaddy, Bago, Myanmar 706

description:
BBL706
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Letpadan, Tharrawaddy, Bago, Myanmar


title: embryo2-3h_E2_H1


title: embryo2-3h_E1_2_F2


title: embryo2-3h_E1_2_G10


title: Bamar from Gyobingauk, Tharrawaddy, Bago, Myanmar 709

description:
BBG709
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo2-3h_E2_D10


title: embryo2-3h_E1_1_D12


title: embryo2-3h_E1_2_H5


title: embryo2-3h_E1_2_F7


title: Bamar from Letpadan, Tharrawaddy, Bago, Myanmar 702

description:
BBL702
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo2-3h_E1_2_F3


title: embryo2-3h_E1_1_A2


title: Bamar from Letpadan, Tharrawaddy, Bago, Myanmar 700

description:
BBL700
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo2-3h_E1_1_D4


title: embryo2-3h_E1_2_E10


title: embryo2-3h_E1_1_B12


title: Bamar from Monyo, Tharrawaddy, Bago, Myanmar 697

description:
BBN697
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Monyo, Tharrawaddy, Bago, Myanmar


title: Bamar from Monyo, Tharrawaddy, Bago, Myanmar 685

description:
BBN685
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo2-3h_E1_1_C6


title: Bamar from Monyo, Tharrawaddy, Bago, Myanmar 688

description:
BBN688
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: embryo2-3h_E1_1_D2


title: Bamar from Monyo, Tharrawaddy, Bago, Myanmar 681

description:
BBN681
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Monyo, Tharrawaddy, Bago, Myanmar 691

description:
BBN691
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Tonbo, Pyay, Bago, Myanmar 667

description:
BBT667
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Tonbo, Pyay, Bago, Myanmar


title: Bamar from Padaung, Pyay, Bago, Myanmar 655

description:
BBP655
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Padaung, Pyay, Bago, Myanmar


title: Bamar from Tonbo, Pyay, Bago, Myanmar 671

description:
BBT671
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Pauk, Pakokku, Magway, Myanmar 635

description:
BMP635
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Pauk, Pakokku, Magway, Myanmar


title: Bamar from Padaung, Pyay, Bago, Myanmar 660

description:
BBP660
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Female


title: kdm5-WT 6

city: Bronx

first: Julie

last: Secombe

address: 1300 Morris park ave

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
Librairies were sequenced on an Illumina HiSeq2500 sequencer (v4 chemistry) using 2 x 50bp cycles.
Alignment of raw reads was carried out using STAR aligner.
Genome_build: dm6.06
Supplementary_files_format_and_content: tab-delimited text files including TPM data for all samples.

source_name: 3rd instar wing disc

growth_protocol: Flies were reared and maintained at 25°C, 50% relative humidity and a 12-hour light/dark cycle

extract_protocol:
RNA was extracted from 3rd instar larval wing discs using Trizol and RNAeasy (Qiagen).
Libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit in accordance with the manufacturer’s instructions. Final libraries were evaluated using fluorescent-based assays including PicoGreen (Life Technologies) or Qubit Fluorometer (invitrogen) and Fragment Analyzer (Advanced Analytics) or BioAnalyzer (Agilent 2100), and were sequenced on an Illumina HiSeq2500 sequencer (v4 chemistry) using 2 x 50bp cycles.

treatment_protocol: larvae were reared in normal growth conditions

value: kdm5 140/kdm5 140;gKDM5:HA WT

tag: devolpmental stage

value: 3rd instar

value: wing disc


title: Bamar from Pauk, Pakokku, Magway, Myanmar 627

description:
BMP627
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Bamar


title: Bamar from Pauk, Pakokku, Magway, Myanmar 628

description:
BMP628
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Pauk, Pakokku, Magway, Myanmar 624

description:
BMP624
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: kdm5-140 6


title: kdm5-WT 5


title: kdm5-WT 1-3


title: kdm5-140 5


title: Bamar from Letpadan, Tharrawaddy, Bago, Myanmar 698

description:
BBL698
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: kdm5-140 1-3


title: Bamar from Pauk, Pakokku, Magway, Myanmar 621

description:
BMP621
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Pauk, Pakokku, Magway, Myanmar 620

description:
BMP620
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: C-49-3

city: Warszawa

first: Aneta

last: Więsyk

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description:
roots at 49 dpi, biological rep3
Gene expression data from pUC9 inoculated roots at 49 dpi

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized on GeneChip Tomato Gene 1.0 ST Array in the Affymetrix according to standard Affymetrix protocol.     scan protocol  GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

scan_protocol: The chips were scanned using the Affymetrix GeneAtlas Scanner.

data_processing: The microarray gene expression data was analyzed using Partek Genomic Suite 6.6 software (Partek Inc., Louis, MO). Raw data (.cel files) were imported and processed, using Robust Multiarray Averaging (RMA) background correction, quantile normalization, Log2 transformation and median polish summarization.

organism: Solanum lycopersicum

source_name: Solanum lycopersicum roots inoculated with pUC9 at 49 dpi

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol.

growth_protocol: Inoculated tomato plants were maintained in a greenhouse at 28-30ºC for 16 h and at 25ºC for 8 h in the dark.

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Kit according to manufacturer’s instruction (Qiagen). Contaminating DNA was removed from the extracted RNA using TURBO DNase-free TM Kit (Ambion).

treatment_protocol: Tomato seedlings with true leaves were mechanically inoculated with purified plasmids (2 μg/plant) containing monomeric full-length cDNAs of PSTVd-M (GenBank nr X76844) or PSTVd-S23 (GenBank nr X76846) and empty pUC9 plasmid as a control. Tomato roots were collected at 17, 24 and 49 days post inoculation.

value: roots

tag: treatment

value: inoculated with pUC9 at 49 dpi

tag: cultivar

value: Rutgers


title: Bamar from Pauk, Pakokku, Magway, Myanmar 612

description:
BMP612
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Pauk, Pakokku, Magway, Myanmar 610

description:
BMP610
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Pauk, Pakokku, Magway, Myanmar 607

description:
BMP607
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Minhla, Thayet, Magway, Myanmar 604

description:
BMT604
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Minhla, Thayet, Magway, Myanmar


title: S-49-2

description:
roots at 49 dpi, biological rep2
Gene expression data from PSTVd-S23 inoculated roots at 49 dpi

source_name: Solanum lycopersicum roots inoculated with PSTVd-S23 at 49 dpi

value: inoculated with PSTVd-S23 at 49 dpi


title: S-49-3

description:
roots at 49 dpi, biological rep3
Gene expression data from PSTVd-S23 inoculated roots at 49 dpi


title: Bamar from Minhla, Thayet, Magway, Myanmar 601

description:
BMT601
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Minhla, Thayet, Magway, Myanmar 603

description:
BMT603
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Minhla, Thayet, Magway, Myanmar 598

description:
BMT598
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Male


title: Bamar from Minhla, Thayet, Magway, Myanmar 597

description:
BMT597
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: S-49-1

description:
roots at 49 dpi, biological rep1
Gene expression data from PSTVd-S23 inoculated roots at 49 dpi


title: Bamar from Minhla, Thayet, Magway, Myanmar 591

description:
BMT591
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: C-49-1

description:
roots at 49 dpi, biological rep1
Gene expression data from pUC9 inoculated roots at 49 dpi


title: Bamar from Minhla, Thayet, Magway, Myanmar 589

description:
BMT589
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: C-49-2

description:
roots at 49 dpi, biological rep2
Gene expression data from pUC9 inoculated roots at 49 dpi


title: Bamar from Kunta, Minbu, Magway, Myanmar 586

description:
BMK586
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Kunta, Minbu, Magway, Myanmar


title: Bamar from Pauk, Pakokku, Magway, Myanmar 615

description:
BMP615
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Pauk, Pakokku, Magway, Myanmar 608

description:
BMP608
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: C-24-1

description:
roots at 24 dpi, biological rep1
Gene expression data from pUC9 inoculated roots at 24 dpi

source_name: Solanum lycopersicum roots inoculated with pUC9 at 24 dpi

value: inoculated with pUC9 at 24 dpi


title: M-49-3

description:
roots at 49 dpi, biological rep3
Gene expression data from PSTVd-M inoculated roots at 49 dpi

source_name: Solanum lycopersicum roots inoculated with PSTVd-M at 49 dpi

value: inoculated with PSTVd-M at 49 dpi


title: M-49-2

description:
roots at 49 dpi, biological rep2
Gene expression data from PSTVd-M inoculated roots at 49 dpi


title: Bamar from Kunta, Minbu, Magway, Myanmar 583

description:
BMK583
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: M-49-1

description:
roots at 49 dpi, biological rep1
Gene expression data from PSTVd-M inoculated roots at 49 dpi


title: S-24-2

description:
roots at 24 dpi, biological rep2
Gene expression data from PSTVd-S23 inoculated roots at 24 dpi

source_name: Solanum lycopersicum roots inoculated with PSTVd-S23 at 24 dpi

value: inoculated with PSTVd-S23 at 24 dpi


title: M-24-3

description:
roots at 24 dpi, biological rep3
Gene expression data from PSTVd-M inoculated roots at 24 dpi

source_name: Solanum lycopersicum roots inoculated with PSTVd-M at 24 dpi

value: inoculated with PSTVd-M at 24 dpi


title: S-24-3

description:
roots at 24 dpi, biological rep3
Gene expression data from PSTVd-S23 inoculated roots at 24 dpi


title: Bamar from Kunta, Minbu, Magway, Myanmar 582

description:
BMK582
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: M-24-1

description:
roots at 24 dpi, biological rep1
Gene expression data from PSTVd-M inoculated roots at 24 dpi


title: Bamar from Kunta, Minbu, Magway, Myanmar 577

description:
BMK577
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: M-24-2

description:
roots at 24 dpi, biological rep2
Gene expression data from PSTVd-M inoculated roots at 24 dpi


title: C-24-3

description:
roots at 24 dpi, biological rep3
Gene expression data from pUC9 inoculated roots at 24 dpi


title: Bamar from Mezali, Minbu, Magway, Myanmar 571

description:
BMM571
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Mezali, Minbu, Magway, Myanmar


title: Bamar from Kunta, Minbu, Magway, Myanmar 575

description:
BMK575
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: S-24-1

description:
roots at 24 dpi, biological rep1
Gene expression data from PSTVd-S23 inoculated roots at 24 dpi


title: Bamar from Mezali, Minbu, Magway, Myanmar 565

description:
BMM565
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Female


title: Bamar from Mezali, Minbu, Magway, Myanmar 563

description:
BMM563
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: C-17-3

description:
roots at 17 dpi, biological rep3
Gene expression data from pUC9 inoculated roots at 17 dpi

source_name: Solanum lycopersicum roots inoculated with pUC9 at 17 dpi

value: inoculated with pUC9 at 17 dpi


title: S-17-2

description:
roots at 17 dpi, biological rep2
Gene expression data from PSTVd-S23 inoculated roots at 17 dpi

source_name: Solanum lycopersicum roots inoculated with PSTVd-S23 at 17 dpi

value: inoculated with PSTVd-S23 at 17 dpi


title: C-17-1

description:
roots at 17 dpi, biological rep1
Gene expression data from pUC9 inoculated roots at 17 dpi


title: C-17-2

description:
roots at 17 dpi, biological rep2
Gene expression data from pUC9 inoculated roots at 17 dpi


title: S-17-1

description:
roots at 17 dpi, biological rep1
Gene expression data from PSTVd-S23 inoculated roots at 17 dpi


title: Bamar from Salin, Minbu, Magway, Myanmar 537

description:
BMS537
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Salin, Minbu, Magway, Myanmar


title: Bamar from Mezali, Minbu, Magway, Myanmar 559

description:
BMM559
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Bamar


title: Bamar from Mezali, Minbu, Magway, Myanmar 545

description:
BMM545
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Mezali, Minbu, Magway, Myanmar 539

description:
BMM539
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Mezali, Minbu, Magway, Myanmar 553

description:
BMM553
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Mezali, Minbu, Magway, Myanmar 557

description:
BMM557
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Mezali, Minbu, Magway, Myanmar 546

description:
BMM546
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Mezali, Minbu, Magway, Myanmar 541

description:
BMM541
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: C-24-2

description:
roots at 24 dpi, biological rep2
Gene expression data from pUC9 inoculated roots at 24 dpi

value: roots


title: Bamar from Salin, Minbu, Magway, Myanmar 525

description:
BMS525
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Salin, Minbu, Magway, Myanmar 531

description:
BMS531
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Salin, Minbu, Magway, Myanmar 519

description:
BMS519
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: M-17-3

description:
roots at 17 dpi, biological rep3
Gene expression data from PSTVd-M inoculated roots at 17 dpi

source_name: Solanum lycopersicum roots inoculated with PSTVd-M at 17 dpi

value: inoculated with PSTVd-M at 17 dpi


title: M-17-2

description:
roots at 17 dpi, biological rep2
Gene expression data from PSTVd-M inoculated roots at 17 dpi

value: Rutgers


title: M-17-1

description:
roots at 17 dpi, biological rep1
Gene expression data from PSTVd-M inoculated roots at 17 dpi


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 508

description:
NSM508
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Naga


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 495

description:
NSM495
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 513

description:
NSM513
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 493

description:
NSM493
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 488

description:
NSM488
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 487

description:
NSM487
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 483

description:
NSM483
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 480

description:
NSM480
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 474

description:
NSH474
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 477

description:
NSM477
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 470

description:
NSH470
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 468

description:
NSH468
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 446

description:
NSH446
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 464

description:
NSH464
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Salin, Minbu, Magway, Myanmar 515

description:
BMS515
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 439

description:
NSL439
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 444

description:
NSL444
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 457

description:
NSH457
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 461

description:
NSH461
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 441

description:
NSL441
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 450

description:
NSH450
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 456

description:
NSH456
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 433

description:
NSL433
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 419

description:
NSL419
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 429

description:
NSL429
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 427

description:
NSL427
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 414 rep 1

description:
NSL414_1
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 389

description:
CCZ389
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Chin

value: Ton Zang, Falam, Chin, Myanmar


title: Chin from Ton Zang, Falam, Chin, Myanmar 388

description:
CCZ388
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 376

description:
CCZ376
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Male


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 453

description:
NSH453
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 366

description:
CCZ366
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 434

description:
NSL434
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 361

description:
CCZ361
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 352

description:
CCZ352
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 414 rep 2

description:
NSL414_2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Naga from Leshi, Naga Self-Administered Zone, Sagaine, Myanmar 422

description:
NSL422
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 347

description:
CCZ347
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 312

description:
CCZ312
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 326

description:
CCZ326
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 338

description:
CCZ338
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 308

description:
CCZ308
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 294

description:
CCZ294
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 296

description:
CCZ296
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 280

description:
CCZ280
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: FAP organoid, HCT24-14

city: Koto-ku

first: Ryoji

last: Yao

state: Tokyo

address: 3-8-31 Ariake

country: Japan

institute: The JFCR-Cancer Institute

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45C on Human U133 plus2.0 micoarray in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with GenePattern (Broad Institute) using default analysis setting and global scailing as normalization method.

source_name: FAP organoid, HCT24-14

label_protocol: Biotinylated cRNA were prepared from 100ng of total RNA using 3' IVT PLUS Kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: Organoids were embedded in Matrigel and cultured in ENR medium.

extract_protocol: Total RNA was isolated using a Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Organoids were recovered from Matrigel using Cell Recovery Sollution (Corning), washed with PBS once and collected by centrifugation.

tag: patient id

value: male

tag: diagnosis

value: CFAP

value: FAP organoid


title: Chin from Ton Zang, Falam, Chin, Myanmar 277

description:
CCZ277
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 324

description:
CCZ324
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: FAP organoid, HCT24-10

source_name: FAP organoid, HCT24-10


title: FAP organoid, HCT24-12

source_name: FAP organoid, HCT24-12


title: Chin from Ton Zang, Falam, Chin, Myanmar 266

description:
CCZ266
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 251

description:
CCZ251
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: FAP organoid, HCT24-11

source_name: FAP organoid, HCT24-11


title: FAP organoid, HCT24-13

source_name: FAP organoid, HCT24-13


title: FAP organoid, HCT24-9

source_name: FAP organoid, HCT24-9


title: Bamar from Pantha, Mawlaik, Sagaine, Myanmar 215

description:
BSP215
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

source_name: blood

value: Pantha, Mawlaik, Sagaine, Myanmar


title: Chin from Ton Zang, Falam, Chin, Myanmar 242

description:
CCZ242
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 227

description:
CCZ227
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Pantha, Mawlaik, Sagaine, Myanmar 217

description:
BSP217
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Pantha, Mawlaik, Sagaine, Myanmar 222

description:
BSP222
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 230

description:
CCZ230
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Ton Zang, Falam, Chin, Myanmar 250

description:
CCZ250
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Pantha, Mawlaik, Sagaine, Myanmar 213

description:
BSP213
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: FAP organoid, HCT24-5

source_name: FAP organoid, HCT24-5


title: Bamar from Pantha, Mawlaik, Sagaine, Myanmar 212

description:
BSP212
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: FAP organoid, HCT24-3

source_name: FAP organoid, HCT24-3


title: FAP organoid, HCT24-4

source_name: FAP organoid, HCT24-4


title: FAP organoid, HCT20-4

source_name: FAP organoid, HCT20-4

value: female


title: Bamar from Pantha, Mawlaik, Sagaine, Myanmar 200

description:
BSP200
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Female


title: Bamar from Pantha, Mawlaik, Sagaine, Myanmar 206

description:
BSP206
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: FAP organoid, HCT23-6

source_name: FAP organoid, HCT23-6

value: AFAP


title: FAP organoid, HCT23-8

source_name: FAP organoid, HCT23-8


title: FAP organoid, HCT20-5

source_name: FAP organoid, HCT20-5


title: FAP organoid, HCT24-6

source_name: FAP organoid, HCT24-6


title: FAP organoid, HCT24-8

source_name: FAP organoid, HCT24-8


title: FAP organoid, HCT20-6

source_name: FAP organoid, HCT20-6


title: FAP organoid, HCT19-13

source_name: FAP organoid, HCT19-13


title: FAP organoid, HCT20-2

source_name: FAP organoid, HCT20-2


title: FAP organoid, HCT24-1

source_name: FAP organoid, HCT24-1


title: FAP organoid, HCT23-7

source_name: FAP organoid, HCT23-7


title: FAP organoid, HCT23-4

source_name: FAP organoid, HCT23-4


title: FAP organoid, HCT24-2

source_name: FAP organoid, HCT24-2


title: FAP organoid, HCT20-3

source_name: FAP organoid, HCT20-3


title: FAP organoid, HCT19-12

source_name: FAP organoid, HCT19-12


title: FAP organoid, HCT19-10

source_name: FAP organoid, HCT19-10


title: Bamar from Pantha, Mawlaik, Sagaine, Myanmar 185

description:
BSP185
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

source_name: blood


title: FAP organoid, HCT24-7

source_name: FAP organoid, HCT24-7


title: FAP organoid, HCT23-5

source_name: FAP organoid, HCT23-5


title: Bamar from Pantha, Mawlaik, Sagaine, Myanmar 189

description:
BSP189
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: FAP organoid, HCT19-9

source_name: FAP organoid, HCT19-9


title: FAP organoid, HCT19-8

source_name: FAP organoid, HCT19-8


title: FAP organoid, HCT19-7

source_name: FAP organoid, HCT19-7


title: Bamar from Pantha, Mawlaik, Sagaine, Myanmar 180

description:
BSP180
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Pantha, Mawlaik, Sagaine, Myanmar 181

description:
BSP181
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: FAP organoid, HCT19-1

source_name: FAP organoid, HCT19-1


title: Chin from Tedim, Falam, Chin, Myanmar 175 rep 2

description:
CCT175_2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Tedim, Falam, Chin, Myanmar


title: Bamar from Pantha, Mawlaik, Sagaine, Myanmar 178

description:
BSP178
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Tedim, Falam, Chin, Myanmar 172

description:
CCT172
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Tedim, Falam, Chin, Myanmar 169

description:
CCT169
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Tedim, Falam, Chin, Myanmar 165

description:
CCT165
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Tedim, Falam, Chin, Myanmar 163

description:
CCT163
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Pantha, Mawlaik, Sagaine, Myanmar 195

description:
BSP195
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Tedim, Falam, Chin, Myanmar 175 rep 1

description:
CCT175
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: FAP organoid, HCT14-9

source_name: FAP organoid, HCT14-9


title: Chin from Tedim, Falam, Chin, Myanmar 159

description:
CCT159
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Tedim, Falam, Chin, Myanmar 154

description:
CCT154
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Tedim, Falam, Chin, Myanmar 173

description:
CCT173
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Tedim, Falam, Chin, Myanmar 158

description:
CCT158
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Tedim, Falam, Chin, Myanmar 148

description:
CCT148
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: FAP organoid, HCT14-4

source_name: FAP organoid, HCT14-4


title: Chin from Tedim, Falam, Chin, Myanmar 152

description:
CCT152
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Tedim, Falam, Chin, Myanmar 146

description:
CCT146
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: FAP organoid, HCT14-5

source_name: FAP organoid, HCT14-5


title: Chin from Tedim, Falam, Chin, Myanmar 139

description:
CCT139
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Tedim, Falam, Chin, Myanmar 141

description:
CCT141
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Tedim, Falam, Chin, Myanmar 135

description:
CCT135
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: FAP organoid, HCT14-8

source_name: FAP organoid, HCT14-8


title: FAP organoid, HCT14-3

source_name: FAP organoid, HCT14-3


title: Chin from Tedim, Falam, Chin, Myanmar 132

description:
CCT132
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: FAP organoid, HCT14-2

source_name: FAP organoid, HCT14-2


title: Chin from Tedim, Falam, Chin, Myanmar 128

description:
CCT128
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: BB1701

city: Aalborg

first: Hanne

last: Due

state: North Region

address: Sdr skovvej 15

department: Department of Hematology

country: Denmark

institute: Aalborg University Hospital

description:
Gene expression data from primary DLBCL tissue samples
ABC/GCB/NC subclass: GCB. Treatment: R-CHOP. IPI score: 0.

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

scan_protocol: Gene Chips HG-U133 Plus 2.0 were scanned using the Affymetrix GeneChip scanner 3000 7G. CEL-files generated using AGCC

data_processing: RMA nomalized using R (v.3.3.3), the affy-package from Bioconductor

label: Biotin

source_name: Primary diffuse large B-cell lymphoma tissue

label_protocol: Affymetrix GeneChip 3' IVT PLUS Reagent Kit (#P/N 902416)

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using a modified protocol combining Trizol reagent (Invitrogen) and mirVana microRNA isolation kit (Ambion/ThermoFisher Scientific)

treatment_protocol: The tumor sample was after removal snap frozen and stored in OCT at -80ºC. From each OCT block, a small fraction of the sample was removed using a scalpel, washed twice in PBS, and homogenized using the TissueLyser II (Qiagen).

tag: abc/gcb/nc subclass

value: GCB

value: R-CHOP

tag: ipi score


title: BB1697

description:
Gene expression data from primary DLBCL tissue samples
ABC/GCB/NC subclass: NC. Treatment: R-CHOP. IPI score: 2.

value: NC


title: Chin from Tedim, Falam, Chin, Myanmar 126

description:
CCT126
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: BB1699

description:
Gene expression data from primary DLBCL tissue samples
ABC/GCB/NC subclass: ABC. Treatment: R-CHOP. IPI score: 2.

value: ABC


title: BB1689


title: BB1688

description:
Gene expression data from primary DLBCL tissue samples
ABC/GCB/NC subclass: GCB. Treatment: R-CHOP. IPI score: 2.


title: Chin from Tedim, Falam, Chin, Myanmar 120

description:
CCT120
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Chin from Tedim, Falam, Chin, Myanmar 118

description:
CCT118
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: BB1700

description:
Gene expression data from primary DLBCL tissue samples
ABC/GCB/NC subclass: ABC. Treatment: R-CHOP. IPI score: 0.


title: BB1698


title: BB1696

description:
Gene expression data from primary DLBCL tissue samples
ABC/GCB/NC subclass: GCB. Treatment: R-CHOP. IPI score: NA.


title: BB1686

description:
Gene expression data from primary DLBCL tissue samples
ABC/GCB/NC subclass: ABC. Treatment: R-CHOP. IPI score: 3.


title: FAP organoid, HCT14-1

source_name: FAP organoid, HCT14-1


title: FAP organoid, HCT14-7

source_name: FAP organoid, HCT14-7


title: BB1685

description:
Gene expression data from primary DLBCL tissue samples
ABC/GCB/NC subclass: ABC. Treatment: R-CHOP. IPI score: 4.


title: BB1679


title: Bamar from Kalemyo, Kale, Sagaine, Myanmar 98

description:
BSK98
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Bamar

value: Kalemyo, Kale, Sagaine, Myanmar


title: Bamar from Kalemyo, Kale, Sagaine, Myanmar 107 rep 1

description:
BSK107
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kalemyo, Kale, Sagaine, Myanmar 105

description:
BSK105
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kalemyo, Kale, Sagaine, Myanmar 101

description:
BSK101
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: BB1677

description:
Gene expression data from primary DLBCL tissue samples
ABC/GCB/NC subclass: NC. Treatment: R-CHOP. IPI score: 3.


title: Bamar from Kalemyo, Kale, Sagaine, Myanmar 112

description:
BSK112
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kalemyo, Kale, Sagaine, Myanmar 94

description:
BSK94
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kalemyo, Kale, Sagaine, Myanmar 107 rep 2

description:
BSK107_2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: BB1675


title: Bamar from Kalemyo, Kale, Sagaine, Myanmar 90

description:
BSK90
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kalemyo, Kale, Sagaine, Myanmar 77

description:
BSK77
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kalemyo, Kale, Sagaine, Myanmar 80

description:
BSK80
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kalemyo, Kale, Sagaine, Myanmar 63

description:
BSK63
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kalemyo, Kale, Sagaine, Myanmar 61

description:
BSK61
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Bamar from Kalemyo, Kale, Sagaine, Myanmar 67

description:
BSK67
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: Rakhine from Satthwa, Thandwe, Rakhine, Myanmar 839

description:
RRS839
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Rakhine

value: Satthwa, Thandwe, Rakhine, Myanmar


title: BB1637

description:
Gene expression data from primary DLBCL tissue samples
ABC/GCB/NC subclass: ABC. Treatment: R-CHOP. IPI score: 3.


title: Bamar from Kyangin, Hinthada, Ayeyarwady, Myanmar 753

description:
BAK753
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Male

value: Kyangin, Hinthada, Ayeyarwady, Myanmar


title: Jingpo from Kachang, Yinjiang, Yunnan, China O2

description:
JYYAO2
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Jingpo

value: Kachang, Yinjiang, Yunnan, China


title: Chin from Tedim, Falam, Chin, Myanmar 119

description:
CCT119
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: Chin


title: African from Nigeria 2

description:
ANA02
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

value: African

value: Nigeria


title: African from Nigeria 3

description:
ANA03
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).


title: HT29-CjInfected-Rep2 (Cj)

city: Galway

first: Michael

last: Cairns

address: University Road

department: NCBES

country: Ireland

institute: NUI Galway

hyb_protocol: All hybridizations were carried out using the hybridization and wash solutions as recommended in the Affymetrix 3' IVT Express Protocol. Carried out by DNA Vision, Charleroi, BE.

scan_protocol: Agilent Technologies Scanner G2505C (5 micron reolution). Carried out by DNA Vision, Charleroi, BE

data_processing: Carried out by DNA Vision, Charleroi, BE. Images were processed using GenePix Pro 6.1.0.4. Spot intensities  were normalized and analyzed in GeneSpring (Ver 12.3). Data were log transformed and quantile normalized. Subsequently all normalized data was baseline transformed to the median of all samples.

label_protocol: Affymetrix 3' IVT Express Protocol. Carried out by DNA Vision, Charleroi, BE starting from 100 ng of eukaryotic RNA

growth_protocol:
[cells] HT29 cells were maintained in flasks in complete Dulbecco's modified Eagle's medium (DMEM) supplemented with 10 % foetal calf serum, 2 mM L-glutamine, 1 % nonessential amino acids and antibiotics (penicillin (50 U/ml) and streptomycin (50 μg/ml). Cells (2 x 106) were seeded on transwell filters (0.4 micometer pore polycarbonate membrane insert) in 6-well plates. Cells were incubated at 37 oC in a humidified 5 % CO2 atmosphere and media was added every second day. TEER measurements were taken at 20 days. Antibiotics were removed from the cells at least 24 h before infection assays.
[bacteria] C. jejuni were plated on Columbia blood agar (Oxoid) plates and grown overnight in a microaerophilic environment using gas packs (Oxoid, BR0038). Bacteria were harvested from plates into Brucella broth and the OD600 adjusted to 0.1 and grown in T25 tissue culture flasks at 37 oC under microaerophilic conditions with shaking at 70-80 rpm until the OD600 reached 0.6. Bacteria were washed twice in PBS and resuspended to an OD600 of 1.8 with antibiotic-free complete DMEM media.

extract_protocol: RNA for microarray hybridisations was isolated by TRIzol extraction followed by standard RNA purification protocols using the RNeasy Mini Kit (Qiagen). RNA quality control was carried by a commercial company (DNA Vision, Charleroi, BE) using an Agilent Bioanalyser 2100. The amount of eukaryotic RNA was corrected across samples using the 28S RNA peak because of the variable presence of prokaryotic RNA (infecting Campylobacter jejuni).

treatment_protocol: On day 20 HT29 cells in transwells were washed with HBSS and 2 ml antibiotic-free complete DMEM media was added to the base of each well and 1 ml of RPMI to the apical surface of each well. On day 21 200µl bacteria (6 x 10^8) were added to each well at an MOI of 300. Plates were incubated at 37 oC for 24 h. Replicate transwells were used to determine the number of bacteria (CFU/ml) that were associated with the cells. Cells were harvested for RNA isolation.

tag: cell line origin

value: Human cell line HT29 was derived originally from an adenocarcinoma of the colon

tag: infection

value: C.jejuni strain 11168


title: E12-CjInfected-Rep1 (Cj)

growth_protocol:
[cells] E12 cells were maintained in flasks in complete Dulbecco's modified Eagle's medium (DMEM) supplemented with 10 % foetal calf serum, 2 mM L-glutamine, 1 % nonessential amino acids and antibiotics (penicillin (50 U/ml) and streptomycin (50 μg/ml). Cells (2 x 106) were seeded on transwell filters (0.4 micometer pore polycarbonate membrane insert) in 6-well plates. Cells were incubated at 37 oC in a humidified 5 % CO2 atmosphere and media was added every second day. TEER measurements were taken at 20 days. Antibiotics were removed from the cells at least 24 h before infection assays.
[bacteria] C. jejuni were plated on Columbia blood agar (Oxoid) plates and grown overnight in a microaerophilic environment using gas packs (Oxoid, BR0038). Bacteria were harvested from plates into Brucella broth and the OD600 adjusted to 0.1 and grown in T25 tissue culture flasks at 37 oC under microaerophilic conditions with shaking at 70-80 rpm until the OD600 reached 0.6. Bacteria were washed twice in PBS and resuspended to an OD600 of 1.8 with antibiotic-free complete DMEM media.

treatment_protocol: On day 20 HT29 cells in transwells were washed with HBSS and 2 ml antibiotic-free complete DMEM media was added to the base of each well and 1 ml of antibiotic-free complete DMEM media to the apical surface of each well. On day 21 200 µl bacteria (6 x 10^8) were added to each well at an MOI of 300. Plates were incubated at 37 oC for 24 h. Replicate transwells were used to determine the number of bacteria (CFU/ml) that were associated with the cells. Cells were harvested for RNA isolation.

value: Derivative of the human cell line HT29 from an original adenocarcinoma of the colon

tag: cell line selection

value: Selected from HT29-MTX on the basis of tight junction formation and adherent mucus production, having many of the characteristics of a gastric cell (Behrens et al., 2001, DOI:10.1023/A:1010974909998)


title: E12-Control-Rep2 (Cj)

value: control


title: E12-CjInfected-Rep2 (Cj)


title: E12-Control-Rep1 (Cj)


title: E12-Control-Rep3 (Cj)


title: HT29-CjInfected-Rep1 (Cj)


title: HT29-Control-Rep1 (Cj)


title: N2_3

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

data_processing:
Fastq files generated by bcl2fastq with adapter trimming
Map to WBcel235 as paired-end using STAR v2.5.2b
Assign uniquely-mapping read-pairs to transcript exons and splice-junctions using Featurecounts v1.5.2
Filter out genes not accruing 10 reads in at least 1 library
Normalize library sizes by TMM
Call differentially expressed genes using Limma Voom
Genome_build: WBcel235
Supplementary_files_format_and_content: degust.tsv; tab-separated table; contains Degust-generated gene-count matrix for samples and Limma-voom estimates for expression levels and significance

organism: Caenorhabditis elegans

source_name: WT_C. elegans whole animal

growth_protocol: Worms were grown on standard NGM plates and fed with E. coli bacteria at 20 degrees celsius

extract_protocol:
RNA was extracted with TRIZOL
RNA was poly-A selected using oligo dT magnetic beads, fragmented and library prepared using TruSeq stranded kit (Illumina)

tag: developmental stage

value: L4 larval stage

tag: genotype/variation

value: WT

value: whole animal


title: Chin from Tedim, Falam, Chin, Myanmar 121

description:
CCT121
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

source_name: blood

value: Female

value: Tedim, Falam, Chin, Myanmar


title: N2_2

tag: tissue


title: HT29-Control-Rep2 (Cj)


title: N2_1


title: mir-1_3

source_name: mir-1_C. elegans whole animal


title: African from Nigeria 1

description:
ANA01
Genomic DNA extracted from normal blood was genotyped using HumanOmniZhongHua-8 BeadChip (Illumina).

tag: gender

value: Male


city: Taipei

last: Hsiao

address: Academia Road, Section 2, Nankang, Taipei, 115, Ta

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description: Gene expression data from CL1-5 cells expressing ALDOA shRNA vector

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

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

source_name: Lung  adenocarcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

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

treatment_protocol: Cell were selected with puromycin for two weeks.  Stably transduced cells were use for this experiment.

tag: cell type

value: Type II alveolar cell

tag: genotype


title: Farmworker_E024

city: Durham

first: Lisa

middle: L

last: Satterwhite

state: North Carolina

address: 101 Science Drive

department: Department of Civil and Environmental Engineering

institute: Duke University

description:
globin-depleted total RNA
2534_116957_HG-U133_PLUS_2_31192_E024.CEL

hyb_protocol: Target was prepared and hybridized according to the “Affymetrix Technical Manual” using a single-round RNA amplification and biotin labeling system (Enzo Life Sciences, Plymouth Meeting, PA).

scan_protocol: Hardware: Affymetrix GC3000 scanner with 7G upgrade, Factory PMT settings. Software: AGCC version 3.1.1, CHP files were scaled using a target intensity of 500.

data_processing: In preparation for statistical analysis, data were normalized onto a single array using the Robust Multichip Average (RMA) algorithm.  The subsequent data were analyzed in log2 form.  Student’s t-test was used to test for differences in gene expression between farmworkers and manual workers on a gene-by-gene basis.  To correct for multiple hypothesis testing, a Bonferroni correction generated the gene expression signature of ten genes.  A false discovery rate (FDR) of 0.01 was used to correct for the multiple hypothesis testing in the farmworker dataset used for pathway analysis.  The Wilcoxon rank-sum test was used to test for differences in urinary metabolite concentration between farmworkers and manual workers; a Bonferroni correction and/or 5% FDR was used to correct for multiple hypothesis testing.  The relationship between each metabolite and each gene was assessed using Spearman’s rho or Pearson correlation coefficient.

source_name: Whole blood

label_protocol: To remove serum beta hemoglobin RNA transcripts, total RNA was incubated with four DNA oligomers whose sequences are complementary to the 3’ portions of the alpha and beta hemoglobin RNA transcripts and formed stable duplex structures with the globin mRNA to block the progression of reverse transcriptase.

extract_protocol: Following consent and completion of the health survey, NC licensed phlebotomists collected in sequence whole blood into an 10 ml purple cap K2EDTA Vacutainer tubes (BD Biosciences, ) and then 10 ml whole blood into a PAXgene tube (PreAnalytiX System, Qiagen, Valencia, CA).  Blood samples were inverted 5 times, stored upright at room temperature for 2 hours during transport, and kept at -80o C until use.

treatment_protocol: not applicable

tag: occupation

value: Farmworker

tag: worker id


title: Farmworker_E025

description:
globin-depleted total RNA
2534_116958_HG-U133_PLUS_2_31193_E025.CEL


title: C32

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

institute: University of Zurich

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were pre-processed using Trimmomatic and Flexbar. Reads were aligned to RGSC Rnor_6.0 genome using STAR aligner with parameters trimLeft=10, minTailQuality=15, minAverageQuality=20, and minReadLength=30.
Aligned reads were converted to gene counts using featureCounts. Outputs for different cells were merged into a single file using custom Python code
Ensembl names were converted to gene names using Ensembl's Rattus_norvegicus.Rnor_6.0.95.gtf file (gene_counts.tsv)
Reads were normalized using scran, and normalized values are stored in normalized_gene_counts.tsv
Genome_build: RGSC Rnor_6.0
Supplementary_files_format_and_content: tab delimited text files. gene_counts.tsv contains raw counts, with genes labeled by their gene names. normalied_gene_counts.tsv contains normalized (scran) counts of cells that passed quality control

organism: Rattus norvegicus

source_name: CA3 Interneuron

extract_protocol:
cytosol aspiration via patch-clamp pipettes
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: rectification

value: RS


title: C31

value: TOR


title: C29


title: FAP organoid, HCT19-3

source_name: FAP organoid, HCT19-3

value: male

value: CFAP

value: FAP organoid


title: Farmworker_E023

description:
globin-depleted total RNA
2534_116956_HG-U133_PLUS_2_31191_E023.CEL


title: CL1-0 cells expressing ALDOA

description: Gene expression data from CL1-0 cells expressing ALDOA vector

value: CL1-0 cells expressing ALDOA vector


title: mir-1_2


title: CL1-0 cells expressing vector control

description: Gene expression data from CL1-0 cells expressing control vector

value: CL1-0 cells expressing vector


title: Farmworker_E020

description:
globin-depleted total RNA
2534_116953_HG-U133_PLUS_2_31188_E020.CEL


title: CL1-5 cells expressing Non-silencing shRNA vector

description: Gene expression data from CL1-5 cells expressing non-silencing shRNA vector


title: C39


title: C49


title: C27


title: Farmworker_E019

description:
globin-depleted total RNA
2534_116952_HG-U133_PLUS_2_31187_E019.CEL


title: mir-1_1


title: Farmworker_E018

description:
globin-depleted total RNA
2534_116951_HG-U133_PLUS_2_31186_E018.CEL


title: Farmworker_E022

description:
globin-depleted total RNA
2534_116955_HG-U133_PLUS_2_31190_E022.CEL


title: C35


title: C24


title: Farmworker_E016

description:
globin-depleted total RNA
2534_116949_HG-U133_PLUS_2_31184_E016.CEL


title: C9


title: C10


title: Farmworker_E017

description:
globin-depleted total RNA
2534_116950_HG-U133_PLUS_2_31185_E017.CEL


title: C7


title: Farmworker_E012

description:
globin-depleted total RNA
2534_116945_HG-U133_PLUS_2_31180_E012.CEL


title: C8


title: Farmworker_E015

description:
globin-depleted total RNA
2534_116948_HG-U133_PLUS_2_31183_E015.CEL


title: C4


title: C5


title: Farmworker_E007

description:
globin-depleted total RNA
2534_116940_HG-U133_PLUS_2_31175_E007.CEL


title: Farmworker_E011

description:
globin-depleted total RNA
2534_116944_HG-U133_PLUS_2_31179_E011.CEL


title: C2


title: Farmworker_E008

description:
globin-depleted total RNA
2534_116941_HG-U133_PLUS_2_31176_E008.CEL


title: Farmworker_E010

description:
globin-depleted total RNA
2534_116943_HG-U133_PLUS_2_31178_E010.CEL


title: C6


title: Farmworker_E004

description:
globin-depleted total RNA
2534_116937_HG-U133_PLUS_2_31172_E004.CEL


title: Hypo_T_ADREX_Ozone_81

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

institute: National Instititute of Environmental Health Sciences

data_processing:
Partek Allignment to Rat Genome
Partek Quantification (Gene) using EM
Genes with < 2 counts across all samples removed
Genes rounded to integers in preparation for DESEQ2
Normalized Counts from DESEQ2
Genome_build: rn6 ensemble release 83
Supplementary_files_format_and_content: Data Matrix of 22587 Genes by 32 Samples (columns) as .CSV

source_name: Hypothalamus

extract_protocol:
Brainstem and hypothalamus were removed, flash frozen on dry ice, and RNA was harvested Direct-Zol RNA MiniPrep kit from Zymo Research (Irvine, CA, USA). Total mRNA was isolated  (Wafergen Biosystems, Fremont, CA, USA) and run in Apollo324 automated sample processing system for mRNA selection. RNA-Seq library was prepared with Wafergen's PrepX mRNA 48 Protocol. cDNA libraries were amplified and dsDNA from each library were quality checked by Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Each library was sequenced according to Illumina NextSeq 500 protocols (1.8 pM + 5% PhiX from Illumina Inc., San Diego, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Wistar Kyoto

value: Hypothalamus

tag: surgery

value: Total Bilateral Adrenalectomy

tag: exposure

value: Ozone (0.8 ppm, 4 hours)

value: 13 weeks old


title: Hypo_T_ADREX_Ozone_82


title: Farmworker_E006

description:
globin-depleted total RNA
2534_116939_HG-U133_PLUS_2_31174_E006.CEL


title: Hypo_T_ADREX_Air_68

value: Air (4 hours)


title: Hypo_T_ADREX_Ozone_84


title: Hypo_T_ADREX_Air_67


title: Farmworker_E003

description:
globin-depleted total RNA
2534_116936_HG-U133_PLUS_2_31171_E003.CEL


title: Hypo_T_ADREX_Air_66


title: Farmworker_E001

description:
globin-depleted total RNA
2534_116934_HG-U133_PLUS_2_31169_E001.CEL


title: Hypo_T_ADREX_Ozone_83


title: Farmworker_E002

description:
globin-depleted total RNA
2534_116935_HG-U133_PLUS_2_31170_E002.CEL


title: Manual_Worker_W024

description:
globin-depleted total RNA
2534_116932_HG-U133_PLUS_2_31167_W024.CEL

value: Manual Worker


title: Manual_Worker_W022

description:
globin-depleted total RNA
2534_116930_HG-U133_PLUS_2_31165_W022.CEL


title: Manual_Worker_W019

description:
globin-depleted total RNA
2534_116927_HG-U133_PLUS_2_31162_W019.CEL


title: Manual_Worker_W021

description:
globin-depleted total RNA
2534_116929_HG-U133_PLUS_2_31164_W021.CEL


title: Manual_Worker_W020

description:
globin-depleted total RNA
2534_116928_HG-U133_PLUS_2_31163_W020.CEL


title: Manual_Worker_W025

description:
globin-depleted total RNA
2534_116933_HG-U133_PLUS_2_31168_W025.CEL


title: Manual_Worker_W023

description:
globin-depleted total RNA
2534_116931_HG-U133_PLUS_2_31166_W023.CEL


title: Hypo_T_SHAM_Ozone_20

value: SHAM


title: Hypo_T_ADREX_Air_65


title: Manual_Worker_W018

description:
globin-depleted total RNA
2534_116926_HG-U133_PLUS_2_31161_W018.CEL


title: Manual_Worker_W014

description:
globin-depleted total RNA
2534_116922_HG-U133_PLUS_2_31157_W014.CEL


title: Manual_Worker_W013

description:
globin-depleted total RNA
2534_116921_HG-U133_PLUS_2_31156_W013.CEL


title: Hypo_T_SHAM_Ozone_19


title: Hypo_T_SHAM_Ozone_17


title: Hypo_T_SHAM_Ozone_18


title: Manual_Worker_W015

description:
globin-depleted total RNA
2534_116923_HG-U133_PLUS_2_31158_W015.CEL


title: Manual_Worker_W010

description:
globin-depleted total RNA
2534_116918_HG-U133_PLUS_2_31153_W010@N2.CEL


title: Manual_Worker_W012

description:
globin-depleted total RNA
2534_116920_HG-U133_PLUS_2_31155_W012@N2.CEL


title: Manual_Worker_W017

description:
globin-depleted total RNA
2534_116925_HG-U133_PLUS_2_31160_W017.CEL


title: Hypo_T_SHAM_Air_3


title: Hypo_T_SHAM_Air_4


title: Manual_Worker_W009

description:
globin-depleted total RNA
2534_116917_HG-U133_PLUS_2_31152_W009.CEL


title: Hypo_T_SHAM_Air_2


title: TKO_RNA_rep2

city: shanghai

first: Yujiang

middle: Geno

last: Shi

address: 131 Dong An Road

department: Institute of Biomedical Science

institute: Fudan university

data_processing:
alignment: tophat (version 2.0.12)
differentally expressed genes calculation: cuffdiff (v2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: cuffdiff output of gene differental expression

source_name: TKO cells

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

extract_protocol:
mRNA purification was carried as manual (61011, Iife technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: multiple myeloma model

value: NSD2 translocation knockout


title: KMS11_RNA_rep2

source_name: KMS11 cells

value: Parental


title: TKO_RNA_rep1


title: KMS11_Input

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

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: antibody


title: TKO_Input


title: KMS11_RNA_rep1


title: Brain_S_ADREX_Air_68

source_name: Brainstem

value: Brainstem


title: Brain_S_ADREX_Ozone_84


title: Brain_S_ADREX_Ozone_83


title: Brain_S_ADREX_Air_67


title: Brain_S_ADREX_Ozone_81


title: Brain_S_ADREX_Air_66


title: Brain_S_ADREX_Ozone_82


title: Brain_S_ADREX_Air_65


title: Brain_S_SHAM_Ozone_20


title: Hypo_T_SHAM_Air_1


title: Brain_S_SHAM_Ozone_18


title: Scramble_S2_4_S36

city: San Francisco

first: Benjamin

last: Huang

state: CA

address: 1450 3rd Street

institute: University of California San Francisco

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 using Bowtie v2
Transcript quantification was performed with RNA-seq by Expectation Maximization (RSEM) protocol.
For publication purposes, sample IDs were renamed as follows: S1=S1, S2=S2, S18=S3, S19=S4, AB1=AB1, AB10=AB2, AB17=AB3, AB22=AB4
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated values files including FPKM values for each sample.

source_name: CCRF-CEM leukemia cell line

growth_protocol: CCRF-CEM cells were cultured as recommended by ATCC guidelines

extract_protocol:
Total RNA was prepared using Trizol based extraction. Samples were purified and concentrated using the RNeasy Mini Kit. RNA concentration was determined using a NanoDrop spectrophotometer. RNA quality was assessed using an Agilent 2200 Bioanalyzer.
Libraries were prepared using the TruSeq RNA Exome RNA kit. Libraries were sequenced on a NextSeq 500 using 150bp paired-end chemistry.

treatment_protocol: Cells were exposed to vehicle, dexamethasone, IL-7, or the combination for 4 or 16 hours

tag: knockout

tag: treatment condition

tag: drug exposure time

value: 16 hours


title: Scramble_S2_6_S35

value: 4 hours


title: Scramble_S2_3_S26


title: Manual_Worker_W007

description:
globin-depleted total RNA
2534_116915_HG-U133_PLUS_2_31150_W007@N2.CEL


title: Scramble_S2_7_S40


title: Scramble_S2_5_S30


title: Brain_S_SHAM_Ozone_19

tag: developmental stage


title: Brain_S_SHAM_Air_4


title: Brain_S_SHAM_Ozone_17


title: Manual_Worker_W004

description:
globin-depleted total RNA
2534_116912_HG-U133_PLUS_2_31147_W004.CEL


title: Scramble_S2_2_S23


title: Manual_Worker_W006

description:
globin-depleted total RNA
2534_116914_HG-U133_PLUS_2_31149_W006@N2.CEL


title: Manual_Worker_W001

description:
globin-depleted total RNA
2534_116909_HG-U133_PLUS_2_31144_W001@N2.CEL


title: Manual_Worker_W005

description:
globin-depleted total RNA
2534_116913_HG-U133_PLUS_2_31148_W005.CEL


title: Brain_S_SHAM_Air_3


title: Scramble_S2_1_S25

value: VEH


title: Brain_S_SHAM_Air_2


title: Scramble_S1_5_S22


title: C23

value: RS


title: Bacteria_rG4seq_P_Li_rep2

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

description:
PA_K_hits.bed
single-ended rG4-seq data of Pseudomonas aeruginosa PAO1 in Li+ rich buffer
instrument model: MiSeq V3 (Illumina).

data_processing:
Bacterial rG4-seq reads were mapped to the P. auruginosa genome by using TopHat (version 2.0.0), with two mismatches allowed
Only the uniquely mapped reads were kept for the subsequent analyses.
Calculate the coverage of each base
Calculate the reverse transcriptase stalling sites
Genome_build: Pseudomonas aeruginosa PAO1 (NC_002516.2) and Escherichia coli str. K-12 substr. MG1655 (NC_000913.3)
Supplementary_files_format_and_content: bed file containing the significant RNA reverse transcriptase stalling sites
Column names:  Refseq, W_Start, W_End, hgnc, RTS_Score,  strand, P_Value, genomic_location, hgnc_genomic_location.
RTS_Score was used to measure the RNA reverse transcriptase stalling degree.

organism: Pseudomonas aeruginosa PAO1

source_name: liquid culture in LB (Luria-Bertani)  medium

growth_protocol: grow until mid-log phase in LB

extract_protocol:
To examine the effect of rG4 sites on the transcriptome of P. auruginosa, 2 ml of mid-log-phase (OD600= 0.6) bacterial LB (Luria-Bertani) cultures (P. auruginosa PAO1strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the Ribo-ZeroTM rRNA Removal Kit (Bacteria) (Epicentre), mRNA was used to generate the cDNA library according to the TruSeq RNA sample prep kit protocol (Illumina), which was then sequenced using the HiSeq 2000 system (Illumina). Bacterial rG4-seq reads were mapped to the P. auruginosa PAO1 (NC_002516.2) genome by using TopHat (version 2.0.0), with two mismatches allowed. Only the uniquely mapped reads were kept for the subsequent analyses.  GO enrich-ment analyses were conducted on all differentially transcribed genes using DAVID before data sets were imported into Cytoscape with an Enrichment Map plugin. The each sample inrG4-seq assay was repeated twice.
TruSeq RNA sample prep kit protocol (Illumina)

value: Wild-type

tag: rts reaction buffer

value: Li


title: Scramble_S1_6_S24


title: Scramble_S1_3_S32


title: Brain_S_SHAM_Air_1

value: Wistar Kyoto

tag: tissue


title: Scramble_S1_4_S31


title: Bacteria_rG4seq_P_K_rep2

description:
PA_K_hits.bed
single-ended rG4-seq data of Pseudomonas aeruginosa PAO1 in K+ rich buffer
instrument model: MiSeq V3 (Illumina).

value: K


title: Bacteria_rG4seq_P_Li_rep1


title: Bacteria_rG4seq_P_K_rep1


title: Scramble_S1_2_S32


title: Scramble_S1_1_S33


title: Scramble_S19_7_S37


title: Hypoxia_med25-1 3

city: Antwerpen

first: Gerrit

last: Beemster

state: Antwerpen

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

data_processing:
Data was processed by CLC genomics workbench vs 9.01
Paired end reads were mapped to the Arabidopsis reference genome (TAIR10) and counts per gene were calculated.
Expression values (counts) were quantile normalised and statistical analysis using Baggerlys test involved pairwise comparisons between wild type and med25 mutant under control and hypoxic conditions, respectively.

organism: Arabidopsis thaliana

source_name: rozettes

growth_protocol: Wildtype and med25-1 seeds were sown on half-strength MS plates + 0.5% sucrose, stratfied for 48 hours at 4°C and germinated at 21°C day / 18°C night with a photoperiod of 16 h light (150 μmol m−2 s−1) and 8 h dark.

extract_protocol:
Total RNA was extracted using the NucleoSpin® RNA Plant kit from Macherey-Nagel according to the manufacturer's  instructions. Subsequently, contaminating DNA was removed using the Turbo DNA-free kit from Ambion according to the manufacturer's instructions.
Sequencing libraries were prepared using the TruSeq® Stranded mRNA HT Sample Preparation kit (Illumina, California, US), following the manufacturer's Low Sample protocol.

treatment_protocol: After 3 weeks, seedlings were exposed to 1% oxygen for 3 hours and immediately frozen in liquid nitrogen.

tag: genotype/variation

value: med25-1 mutant

tag: treatment

value: Hypoxia


title: Scramble_S19_5_S45


title: Hypoxia_med25-1 1


title: Hypoxia_med25-1 2


title: Scramble_S1_7_S27


title: Control_med25-1 2

value: Control conditions


title: Scramble_S19_2_S38


title: Scramble_S19_1_S40


title: Hypoxia_wildtype 2

value: wild type


title: Scramble_S19_4_S29


title: Scramble_S19_3_S33


title: Control_wildtype 3


title: Control_med25-1 3


title: Hypoxia_wildtype 1


title: Scramble_S18_5_S48


title: Control_med25-1 1


title: Control_wildtype 1


title: Scramble_S18_6_S34


title: active bear_paired-end_reads

city: Berlin

first: Xintian

middle: Arthur

last: YOU

address: Robert-Roessle-str. 10

country: Germany

institute: Max-Delbrueck-Center for Molecular Medicine

description: paired-end reads are from bear named "Star"

data_processing:
Basecalls performed using Illumina RTA, version 1.6.32.0
454 reads were pre-assembled using Roche Newbler version 2.3
Paired-end Illumina reads were pre-assembled using SOAPdenovo version 1.3
Final transcript set was assembled using Roche Newbler version 2.3 using pre-assembled 454 contigs and pre-assembled Illumina contigs
Single-end Illumina reads were aligned to final transcript set using SOAP2 with default parameters
Supplementary_files_format_and_content: fasta file for the final transcript set and tab-delimited file for transcript expression (measured in RPKM)

organism: Ursus arctos

extract_protocol:
Total RNA from grizzly bear muscle was isolated using the standard TRIzol protocol (Invitrogen) with an additional 70% ethanol precipitation step in the end. Poly(A) RNA was then purified by two rounds of selection using the Dynabeads mRNA Purification Kit (Invitrogen) according to the manufacturer’s instructions and quantified by Nanodrop 7500 spectrophotometer. Sample quality was assessed by Bioanalyzer (Agilent Technologies).
The construction of normalized full-length-enriched cDNA libraries for 454 sequencing requires three steps: (1) the synthesis of double strand cDNA using a modified RACE technique, (2) the subsequent removal of poly(A):T tails using the methylation sensitive type II restriction enzyme GsuI, followed by the ligation of a new DNA adaptor, and (3) the normalization of the resulting cDNA library using duplex-specific nuclease (DSN). The DSN normalization method is based on the denaturation–reassociation of double-stranded (ds) cDNA coupled with the degradation of the ds cDNA fraction formed by abundant transcripts (Shagin et al. 2002; Zhulidov et al. 2004) and requires the presence of adaptor sequences at each terminus of the cDNA to prime PCR amplification.

value: adult (10 years)

value: gastrocnemius muscle

tag: hibernation status

value: non-hibernating (active)


title: hibernating bear_paired-end_reads

value: hibernating


title: Hypoxia_wildtype 3


title: WT rep2

city: Houston

first: Peng

last: Tan

state: TX

address: 6670 Bertner Ave, R9-460

institute: Houston Methodist Research Institute

data_processing:
Base-calling was performed on Ion Torrent suite software.
Raw sequencing reads in FASTQ format were aligned to the UCSC mouse reference genome (mm10) using TOPHAT21
Differentially expressed genes were identified using DESeq2 version 1.62. Only genes with a minimum fold change of +/− 2, a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were classified as having significant differential expression.
Gene set enrichment analysis (GSEA) software was used to perform GSEA against the GSEA database was used
The DAVID/EASE software (https://david.ncifcrf.gov/summary.jsp) was used to establish whether specific cell functions and biologic processes, defined according to gene ontology, were significantly represented among the deregulated genes.
Genome_build: mm10
Supplementary_files_format_and_content: Text files include raw reads and RPKM values for each Sample.

organism: Mus musculus

source_name: Cervical lymph node

extract_protocol:
Cervical lymph nodes or cervical lymphomas were removed, flash frozen on dry ice. Total RNA was used for mRNA isolation and cDNA library generation with miRNeasy micro Kit (Qiagen). On-column DNase digestion (DNase-Free DNase Set, Qiagen) was performed according to manufacturer protocols to prevent genomic DNA contamination.
RNA and library preparation integrity were verified using a 2100 BioAnalyzer system (Agilent). Ribosomal RNA depletion was performed following the low input protocol by RiboMinus Eukaryote System v2 (ThermoFisher) with 500 ng total RNA input. Finally, libraries were prepared using the Ion Total RNA-Seq Kit v2 (ThermoFisher) with minor changes to the standard protocol. These included lower amplification cycles and the usage of entire fragmented RNA for cDNA synthesis.

value: Cervical lymph node

tag: age

value: post natal week 20

tag: genotype


title: Scramble_S19_6_S41

value: 4 hours


title: Scramble_S18_1_S43

value: VEH


title: Becn1-M-KO rep2

value: Becn1 KO


title: STAT5_KO_AB22_7_S55

value: STAT5A and STAT5B


title: Scramble_S18_4_S28

value: 16 hours


title: Scramble_S18_3_S36


title: Becn1-M-KO rep1


title: WT rep1


title: Scramble_S18_7_S42


title: Control_wildtype 2


title: STAT5_KO_AB22_3_S52


title: STAT5_KO_AB22_5_S37


title: STAT5_KO_AB22_4_S51


title: STAT5_KO_AB22_2_S47