title: KH003-046-207970

description:
KH003-046-207970
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-046


title: KH003-043-202540

status: Public on Jul 15 2014

type: RNA

city: Singapore

first: Sachel

last: Mok

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

description:
KH003-043-202540
Reference sample is laboratory strain 3D7.

hyb_protocol: Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 65°C in a rotating hybridization oven at 10rpm.

scan_protocol: Microarray scanning was done using PowerScanner (Tecan, Austria) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments, USA) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.

data_processing: Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel passed quality control and were accepted. Local background correction using normexp, followed by lowess normalization across all features were carried out to generate the normalized Log2 gene expression ratios.

molecule: total RNA

organism: Plasmodium falciparum

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-043

label_protocol: Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with Cy fluorophore were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

tag: culture

value: in vivo

tag: Stage

value: blood

tag: patient sample id

tag: geographic origin

value: Rattanakiri, Cambodia

tag: barcode

tag: timepoint

value: prior to artemisinin combination therapy (ACT)

tag: parasite clearance halflife upon artemisinin treatment (h)

source_name: P. falciparum 3D7 RNA reference pool

tag: strain/background

value: In vitro

value: asexual blood

tag: composition

value: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle

tag: sample type

value: reference


title: KH003-045-207965

description:
KH003-045-207965
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-045


title: KH003-044-202700

description:
KH003-044-202700
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-044


title: KH003-033-202675

description:
KH003-033-202675
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-033


title: KH003-042-202692

description:
KH003-042-202692
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-042


title: KH003-034-188599

description:
KH003-034-188599
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-034


title: KH003-041-202693

description:
KH003-041-202693
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-041


title: KH003-038-202516

description:
KH003-038-202516
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-038


title: KH003-036-202681

description:
KH003-036-202681
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-036


title: KH003-039-202687

description:
KH003-039-202687
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-039


title: KH003-035-202494

description:
KH003-035-202494
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-035


title: KH003-037-202682

description:
KH003-037-202682
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-037


title: KH003-031-202667

description:
KH003-031-202667
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-031


title: KH003-028-199071

description:
KH003-028-199071
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-028


title: KH003-032-202477

description:
KH003-032-202477
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-032


title: KH003-027-199029

description:
KH003-027-199029
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-027


title: KH003-051-208021

description:
KH003-051-208021
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-051


title: KH003-040-202686

description:
KH003-040-202686
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-040

source_name: P. falciparum 3D7 RNA reference pool


title: KH003-025-198651

description:
KH003-025-198651
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-025


title: KH003-029-202663

description:
KH003-029-202663
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-029


title: KH003-024-198650

description:
KH003-024-198650
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-024


title: KH003-022-198647

description:
KH003-022-198647
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-022


title: KH003-030-202662

description:
KH003-030-202662
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-030


title: KH003-021-199016

description:
KH003-021-199016
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-021


title: KH003-020-199012

description:
KH003-020-199012
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-020


title: KH003-019-199011

description:
KH003-019-199011
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-019


title: KH003-017-198995

description:
KH003-017-198995
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-017


title: KH003-018-199002

description:
KH003-018-199002
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-018


title: KH003-015-198991

description:
KH003-015-198991
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-015


title: KH003-016-198993

description:
KH003-016-198993
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-016


title: KH003-009-188531

description:
KH003-009-188531
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-009


title: KH002-120-216557

description:
KH002-120-216557
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-120

value: Preah Vihear, Cambodia


title: KH003-013-198988

description:
KH003-013-198988
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-013


title: KH003-004-188680

description:
KH003-004-188680
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-004


title: KH002-115-236424

description:
KH002-115-236424
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-115

source_name: P. falciparum 3D7 RNA reference pool


title: KH002-112-236438

description:
KH002-112-236438
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-112


title: KH002-109-236376

description:
KH002-109-236376
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-109


title: KH003-010-188537

description:
KH003-010-188537
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-010


title: KH003-011-188708

description:
KH003-011-188708
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-011


title: KH003-012-198592

description:
KH003-012-198592
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Rattanakiri Cambodia, KH003-012


title: KH002-105-236131

description:
KH002-105-236131
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-105


title: KH002-110-236379

description:
KH002-110-236379
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-110


title: KH002-116-236416

description:
KH002-116-236416
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-116


title: KH002-104-236092

description:
KH002-104-236092
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-104


title: KH002-118-216558

description:
KH002-118-216558
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-118


title: KH002-103-236084

description:
KH002-103-236084
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-103


title: KH002-107-236172

description:
KH002-107-236172
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-107


title: KH002-106-236170

description:
KH002-106-236170
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-106


title: KH002-117-216493

description:
KH002-117-216493
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-117


title: KH002-108-236175

description:
KH002-108-236175
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-108


title: KH002-119-216571

description:
KH002-119-216571
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-119


title: KH002-102-236274

description:
KH002-102-236274
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-102

source_name: P. falciparum 3D7 RNA reference pool


title: KH002-100-236260

description:
KH002-100-236260
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-100


title: KH002-101-236262

description:
KH002-101-236262
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-101


title: KH002-114-236427

description:
KH002-114-236427
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-114


title: KH002-098-236247

description:
KH002-098-236247
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-098


title: KH002-111-236447

description:
KH002-111-236447
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-111


title: KH002-099-236258

description:
KH002-099-236258
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-099


title: KH002-094-213785

description:
KH002-094-213785
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-094


title: KH002-095-213793

description:
KH002-095-213793
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-095


title: KH002-092-213764

description:
KH002-092-213764
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-092


title: KH002-096-213808

description:
KH002-096-213808
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-096


title: KH002-089-213743

description:
KH002-089-213743
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-089


title: KH002-085-198163

description:
KH002-085-198163
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-085


title: KH002-088-198182

description:
KH002-088-198182
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-088


title: KH002-086-198165

description:
KH002-086-198165
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-086


title: KH002-093-236214

description:
KH002-093-236214
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-093


title: KH002-081-207358

description:
KH002-081-207358
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-081


title: KH002-097-213810

description:
KH002-097-213810
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-097

source_name: P. falciparum 3D7 RNA reference pool


title: KH002-087-198173

description:
KH002-087-198173
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-087


title: KH002-084-198161

description:
KH002-084-198161
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-084


title: KH002-090-213751

description:
KH002-090-213751
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-090


title: KH002-082-198157

description:
KH002-082-198157
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-082


title: KH002-091-213753

description:
KH002-091-213753
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-091


title: KH002-083-198159

description:
KH002-083-198159
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-083


title: KH002-073-198252

description:
KH002-073-198252
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-073


title: KH002-072-198243

description:
KH002-072-198243
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-072


title: KH002-071-198234

description:
KH002-071-198234
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-071


title: KH002-078-207339

description:
KH002-078-207339
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-078


title: KH002-079-207341

description:
KH002-079-207341
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-079


title: KH002-060-207322

description:
KH002-060-207322
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-060


title: KH002-061-207324

description:
KH002-061-207324
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-061


title: KH002-063-207336

description:
KH002-063-207336
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-063


title: KH002-077-198275

description:
KH002-077-198275
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-077


title: KH002-052-207468

description:
KH002-052-207468
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-052


title: KH002-064-198185

description:
KH002-064-198185
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-064

source_name: P. falciparum 3D7 RNA reference pool


title: KH002-062-207334

description:
KH002-062-207334
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-062


title: KH002-053-207470

description:
KH002-053-207470
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-053


title: KH002-065-198187

description:
KH002-065-198187
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-065


title: KH002-054-207480

description:
KH002-054-207480
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-054


title: KH002-076-198273

description:
KH002-076-198273
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-076


title: KH002-059-207313

description:
KH002-059-207313
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-059


title: KH002-067-198205

description:
KH002-067-198205
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-067


title: KH002-069-198216

description:
KH002-069-198216
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-069


title: KH002-058-207311

description:
KH002-058-207311
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-058


title: KH002-070-198225

description:
KH002-070-198225
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-070


title: KH002-055-207496

description:
KH002-055-207496
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-055


title: KH002-050-207450

description:
KH002-050-207450
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-050


title: KH002-057-207302

description:
KH002-057-207302
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-057


title: KH002-049-207448

description:
KH002-049-207448
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-049


title: KH002-066-198196

description:
KH002-066-198196
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-066


title: KH002-056-207488

description:
KH002-056-207488
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-056


title: KH002-068-198207

description:
KH002-068-198207
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-068

source_name: P. falciparum 3D7 RNA reference pool


title: KH002-048-198573

description:
KH002-048-198573
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-048


title: KH002-044-207295

description:
KH002-044-207295
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-044


title: KH002-074-198261

description:
KH002-074-198261
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-074


title: KH002-051-207459

description:
KH002-051-207459
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-051


title: KH002-046-207297

description:
KH002-046-207297
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-046


title: KH002-042-198584

description:
KH002-042-198584
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-042


title: KH002-047-207446

description:
KH002-047-207446
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-047


title: KH002-041-198562

description:
KH002-041-198562
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-041


title: KH002-045-198574

description:
KH002-045-198574
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-045


title: KH002-043-198564

description:
KH002-043-198564
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-043


title: KH002-040-198560

description:
KH002-040-198560
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-040


title: KH002-039-198551

description:
KH002-039-198551
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-039


title: KH002-075-198270

description:
KH002-075-198270
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-075


title: KH002-032-198516

description:
KH002-032-198516
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-032


title: KH002-031-198514

description:
KH002-031-198514
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-031


title: KH002-038-198542

description:
KH002-038-198542
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-038


title: KH002-037-198540

description:
KH002-037-198540
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-037

source_name: P. falciparum 3D7 RNA reference pool


title: KH002-033-198525

description:
KH002-033-198525
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-033


title: KH002-036-198538

description:
KH002-036-198538
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-036


title: KH002-020-188408

description:
KH002-020-188408
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-020


title: KH002-035-198536

description:
KH002-035-198536
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-035


title: KH002-034-198527

description:
KH002-034-198527
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-034


title: KH002-021-188492

description:
KH002-021-188492
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-021


title: KH002-019-188409

description:
KH002-019-188409
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-019


title: KH002-023-198471

description:
KH002-023-198471
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-023


title: KH002-016-188365

description:
KH002-016-188365
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-016


title: KH002-028-198487

description:
KH002-028-198487
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-028


title: KH002-013-188470

description:
KH002-013-188470
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-013


title: KH002-015-188364

description:
KH002-015-188364
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-015


title: KH002-025-198484

description:
KH002-025-198484
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-025


title: KH002-029-198499

description:
KH002-029-198499
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-029


title: KH002-017-188367

description:
KH002-017-188367
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-017


title: KH002-030-198496

description:
KH002-030-198496
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-030


title: KH002-022-188489

description:
KH002-022-188489
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-022

source_name: P. falciparum 3D7 RNA reference pool


title: KH002-018-188406

description:
KH002-018-188406
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-018


title: KH002-024-198476

description:
KH002-024-198476
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-024


title: KH002-008-188452

description:
KH002-008-188452
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-008


title: KH002-009-188455

description:
KH002-009-188455
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-009


title: KH002-027-198486

description:
KH002-027-198486
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-027


title: KH002-014-188359

description:
KH002-014-188359
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-014


title: KH002-012-188468

description:
KH002-012-188468
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-012


title: KH002-010-188458

description:
KH002-010-188458
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-010


title: KH002-011-188464

description:
KH002-011-188464
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-011


title: KH001-120-236363

description:
KH001-120-236363
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-120

value: Pursat, Cambodia


title: KH001-117-236300

description:
KH001-117-236300
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-117


title: KH002-006-188440

description:
KH002-006-188440
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-006


title: KH002-003-188428

description:
KH002-003-188428
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-003


title: KH002-001-188418

description:
KH002-001-188418
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-001


title: KH002-005-188439

description:
KH002-005-188439
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-005


title: KH001-116-236285

description:
KH001-116-236285
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-116


title: KH001-114-215759

description:
KH001-114-215759
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-114

source_name: P. falciparum 3D7 RNA reference pool


title: KH002-002-188426

description:
KH002-002-188426
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-002


title: KH001-118-236292

description:
KH001-118-236292
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-118


title: KH001-119-236308

description:
KH001-119-236308
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-119


title: KH001-109-216402

description:
KH001-109-216402
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-109


title: KH001-113-217468

description:
KH001-113-217468
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-113


title: KH001-108-216395

description:
KH001-108-216395
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-108


title: KH001-110-216407

description:
KH001-110-216407
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-110


title: KH001-111-217165

description:
KH001-111-217165
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-111


title: KH001-112-217466

description:
KH001-112-217466
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-112


title: KH001-106-216385

description:
KH001-106-216385
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-106


title: KH001-107-216391

description:
KH001-107-216391
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-107


title: KH001-103-202074

description:
KH001-103-202074
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-103


title: KH001-101-202097

description:
KH001-101-202097
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-101


title: KH001-104-216376

description:
KH001-104-216376
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-104


title: KH001-102-202073

description:
KH001-102-202073
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-102


title: KH001-099-194524

description:
KH001-099-194524
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-099


title: KH001-097-194553

description:
KH001-097-194553
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-097

source_name: P. falciparum 3D7 RNA reference pool


title: KH001-098-194550

description:
KH001-098-194550
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-098


title: KH001-096-194503

description:
KH001-096-194503
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-096


title: KH001-100-202110

description:
KH001-100-202110
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-100


title: KH001-093-194468

description:
KH001-093-194468
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-093


title: KH001-094-194474

description:
KH001-094-194474
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-094


title: KH001-087-202323

description:
KH001-087-202323
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-087


title: KH001-092-194459

description:
KH001-092-194459
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-092


title: KH001-083-202293

description:
KH001-083-202293
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-083


title: KH001-089-202328

description:
KH001-089-202328
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-089


title: KH001-081-202283

description:
KH001-081-202283
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-081


title: KH001-090-202340

description:
KH001-090-202340
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-090


title: KH001-078-208435

description:
KH001-078-208435
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-078


title: KH001-082-202288

description:
KH001-082-202288
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-082


title: KH001-079-202262

description:
KH001-079-202262
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-079


title: KH001-095-194491

description:
KH001-095-194491
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-095


title: KH001-084-202303

description:
KH001-084-202303
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-084


title: KH001-080-202274

description:
KH001-080-202274
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-080

source_name: P. falciparum 3D7 RNA reference pool


title: KH001-091-202353

description:
KH001-091-202353
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-091


title: KH001-086-202310

description:
KH001-086-202310
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-086


title: KH001-077-208433

description:
KH001-077-208433
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-077


title: KH001-076-208424

description:
KH001-076-208424
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-076


title: KH001-072-188104

description:
KH001-072-188104
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-072


title: KH001-088-202330

description:
KH001-088-202330
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-088


title: KH001-075-208422

description:
KH001-075-208422
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-075


title: KH001-071-188102

description:
KH001-071-188102
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-071


title: KH001-070-188101

description:
KH001-070-188101
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-070


title: KH001-069-188098

description:
KH001-069-188098
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-069


title: KH001-067-188087

description:
KH001-067-188087
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-067


title: KH001-065-188075

description:
KH001-065-188075
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-065


title: KH001-063-193825

description:
KH001-063-193825
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-063


title: KH001-064-188073

description:
KH001-064-188073
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-064


title: KH001-062-188068

description:
KH001-062-188068
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-062


title: KH001-049-194037

description:
KH001-049-194037
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-049


title: KH001-105-216377

description:
KH001-105-216377
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-105

source_name: P. falciparum 3D7 RNA reference pool


title: KH001-047-199363

description:
KH001-047-199363
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-047


title: KH001-068-188096

description:
KH001-068-188096
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-068


title: KH001-066-188082

description:
KH001-066-188082
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-066


title: KH001-060-188056

description:
KH001-060-188056
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-060


title: KH001-051-199356

description:
KH001-051-199356
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-051


title: KH001-054-193799

description:
KH001-054-193799
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-054


title: KH001-055-194051

description:
KH001-055-194051
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-055


title: KH001-052-193787

description:
KH001-052-193787
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-052


title: KH001-056-193812

description:
KH001-056-193812
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-056


title: KH001-059-193849

description:
KH001-059-193849
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-059


title: KH001-048-194024

description:
KH001-048-194024
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-048


title: KH001-061-193838

description:
KH001-061-193838
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-061


title: KH001-058-193822

description:
KH001-058-193822
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-058


title: KH001-057-193821

description:
KH001-057-193821
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-057


title: KH001-044-194008

description:
KH001-044-194008
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-044


title: KH001-046-199364

description:
KH001-046-199364
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-046


title: KH001-043-199352

description:
KH001-043-199352
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-043

source_name: P. falciparum 3D7 RNA reference pool


title: KH001-041-193987

description:
KH001-041-193987
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-041


title: KH001-040-193974

description:
KH001-040-193974
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-040


title: KH002-007-188442

description:
KH002-007-188442
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Preah Vihear Cambodia, KH002-007


title: KH001-034-193757

description:
KH001-034-193757
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-034


title: KH001-026-194314

description:
KH001-026-194314
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-026


title: KH001-032-199343

description:
KH001-032-199343
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-032


title: KH001-031-199342

description:
KH001-031-199342
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-031


title: KH001-015-188181

description:
KH001-015-188181
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-015


title: KH001-030-199332

description:
KH001-030-199332
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-030


title: KH001-018-188173

description:
KH001-018-188173
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-018


title: KH001-013-188144

description:
KH001-013-188144
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-013


title: KH001-025-194306

description:
KH001-025-194306
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-025


title: KH001-017-188174

description:
KH001-017-188174
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-017


title: KH001-020-194265

description:
KH001-020-194265
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-020


title: KH001-028-194335

description:
KH001-028-194335
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-028


title: KH001-038-193778

description:
KH001-038-193778
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-038


title: KH001-021-194272

description:
KH001-021-194272
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-021

source_name: P. falciparum 3D7 RNA reference pool


title: str_7211_+Pi_T96h_rep1

city: Corvallis

first: Paul

last: Carini

address: 220 NASH hall

country: USA

institute: Oregon State U

description: 100 uM phosphate added_96 h

hyb_protocol: 10 µg of labeled aRNA was hybridized to chips at 45˚C, rotating at 60 rpm for 16 hours.

scan_protocol: The samples were scanned with an Affymetrix GeneChip Scanner 3000 7G with autoloader using AGCC software.

data_processing: RMA normalization conducted with Affymetrix ExpressionConsole software package.

label: biotin

organism: Candidatus Pelagibacter sp. HTCC7211

source_name: Phosphate replete P. ubique str. 7211 time point 96 h rep 1

label_protocol: RNA was labeled with biotin labeled nucleotides during the in-vitro transcription reaction.

growth_protocol: Artificial seawater media (AMS1 Carini et al., 2013) with no additional (Limited) or 1 µM (Control) Thiamine, 1.M oxaloacetate, 50 µM Methionine, 50 µM Glycine, 10 µM phosphate, and trace metals. Cells were grown at 20 °C in the dark with gentle agitation.

extract_protocol: Total RNA was extracted using RNeasy Kit (Qiagen) and amplified using MessageAmp-II-Bacteria RNA Amplification Kit (Ambion).

treatment_protocol: 15 ml of culture from each biological replicate were harvested via centrifugation (1 hour at 43 000 g, 10°C), then re-suspended in 1 ml of Bacteria Protect (Qiagen) for 15 min. Following RNA stabilization, cells were collected by centrifugation (30 min at 40 000 g, 10°C), the supernatant was removed, and cells were then stored frozen at -80°C prior to extraction.

tag: strain


title: KH001-029-194349

description:
KH001-029-194349
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-029


title: KH001-022-194286

description:
KH001-022-194286
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-022


title: KH001-039-193972

description:
KH001-039-193972
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-039


title: str_7211_+Pi_T96h_rep2

description: 100 uM phosphate added_96 h

source_name: Phosphate replete P. ubique str. 7211 time point 96 h rep 2


title: KH001-036-193959

description:
KH001-036-193959
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-036


title: str_7211_noPi_T96h_rep3

description: No phosphate added_96 h

source_name: Phosphate deplete P. ubique str. 7211 time point 96 h rep 3


title: str_7211_+Pi_T96h_rep3

description: 100 uM phosphate added_96 h

source_name: Phosphate replete P. ubique str. 7211 time point 96 h rep 3


title: str_7211_noPi_T96h_rep2

description: No phosphate added_96 h

source_name: Phosphate deplete P. ubique str. 7211 time point 96 h rep 2


title: KH001-016-188176

description:
KH001-016-188176
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-016


title: KH001-023-194291

description:
KH001-023-194291
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-023


title: str_7211_noPi_T96h_rep1

description: No phosphate added_96 h

source_name: Phosphate deplete P. ubique str. 7211 time point 96 h rep 1


title: KH001-024-194298

description:
KH001-024-194298
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-024


title: str_7211_+Pi_T68h_rep2

description: 100 uM phosphate added_68 h

source_name: Phosphate replete P. ubique str. 7211 time point 68 h rep 2


title: KH001-007-188129

description:
KH001-007-188129
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-007


title: KH001-012-188198

description:
KH001-012-188198
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-012


title: KH001-006-188127

description:
KH001-006-188127
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-006

source_name: P. falciparum 3D7 RNA reference pool


title: str_7211_+Pi_T68h_rep1

description: 100 uM phosphate added_68 h

source_name: Phosphate replete P. ubique str. 7211 time point 68 h rep 1


title: KH001-011-188204

description:
KH001-011-188204
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-011


title: KH001-004-188209

description:
KH001-004-188209
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-004


title: str_7211_noPi_T38h_rep3

description: No phosphate added_38 h

source_name: Phosphate deplete P. ubique str. 7211 time point 38 h rep 3


title: str_7211_+Pi_T38h_rep2

description: 100 uM phosphate added_38 h

source_name: Phosphate replete P. ubique str. 7211 time point 38 h rep 2


title: str_7211_+Pi_T38h_rep3

description: 100 uM phosphate added_38 h

source_name: Phosphate replete P. ubique str. 7211 time point 38 h rep 3


title: KH001-005-188208

description:
KH001-005-188208
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-005


title: str_7211_noPi_T68h_rep2

description: No phosphate added_68 h

source_name: Phosphate deplete P. ubique str. 7211 time point 68 h rep 2


title: KH001-001-188118

description:
KH001-001-188118
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-001


title: str_7211_+Pi_T20h_rep2

description: 100 uM phosphate added_20 h

source_name: Phosphate replete P. ubique str. 7211 time point 20 h rep 2


title: CD001-120-254449

description:
CD001-120-254449
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-120

value: Kinshasa, DRCongo


title: str_7211_noPi_T68h_rep1

description: No phosphate added_68 h

source_name: Phosphate deplete P. ubique str. 7211 time point 68 h rep 1


title: str_7211_noPi_T38h_rep1

description: No phosphate added_38 h

source_name: Phosphate deplete P. ubique str. 7211 time point 38 h rep 1


title: str_7211_+Pi_T20h_rep3

description: 100 uM phosphate added_20 h

source_name: Phosphate replete P. ubique str. 7211 time point 20 h rep 3


title: CD001-115-254614

description:
CD001-115-254614
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-115


title: CD001-117-254487

description:
CD001-117-254487
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-117


title: CD001-118-254483

description:
CD001-118-254483
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-118

source_name: P. falciparum 3D7 RNA reference pool


title: str_7211_noPi_T38h_rep2

description: No phosphate added_38 h

source_name: Phosphate deplete P. ubique str. 7211 time point 38 h rep 2


title: str_7211_+Pi_T68h_rep3

description: 100 uM phosphate added_68 h

source_name: Phosphate replete P. ubique str. 7211 time point 68 h rep 3


title: CD001-119-254451

description:
CD001-119-254451
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-119


title: str_7211_noPi_T68h_rep3

description: No phosphate added_68 h

source_name: Phosphate deplete P. ubique str. 7211 time point 68 h rep 3


title: str_7211_+Pi_T38h_rep1

description: 100 uM phosphate added_38 h

source_name: Phosphate replete P. ubique str. 7211 time point 38 h rep 1


title: KH001-074-208412

description:
KH001-074-208412
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-074


title: KH001-073-208405

description:
KH001-073-208405
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Pursat Cambodia, KH001-073


title: CD001-116-254494

description:
CD001-116-254494
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-116


title: CD001-113-254612

description:
CD001-113-254612
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-113


title: CD001-112-254588

description:
CD001-112-254588
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-112


title: str_7211_noPi_T20h_rep3

description: No phosphate added_20 h

source_name: Phosphate deplete P. ubique str. 7211 time point 20 h rep 3


title: CD001-110-254584

description:
CD001-110-254584
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-110


title: str_7211_noPi_T20h_rep2

description: No phosphate added_20 h

source_name: Phosphate deplete P. ubique str. 7211 time point 20 h rep 2


title: str_7211_noPi_T20h_rep1

description: No phosphate added_20 h

source_name: Phosphate deplete P. ubique str. 7211 time point 20 h rep 1


title: CD001-114-254613

description:
CD001-114-254613
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-114


title: str_7211_+Pi_T20h_rep1

description: 100 uM phosphate added_20 h

source_name: Phosphate replete P. ubique str. 7211 time point 20 h rep 1


title: CD001-104-255101

description:
CD001-104-255101
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-104

source_name: P. falciparum 3D7 RNA reference pool


title: CD001-111-254585

description:
CD001-111-254585
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-111


title: str_1062_noPi_T38h_rep3

description: No phosphate added_38 h

organism: Candidatus Pelagibacter ubique HTCC1062

source_name: Phosphate deplete P. ubique str. HTCC1062 time point 38 h rep 3


title: CD001-103-255097

description:
CD001-103-255097
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-103


title: CD001-108-254542

description:
CD001-108-254542
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-108


title: CD001-105-255100

description:
CD001-105-255100
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-105


title: str_7211_+Pi_T0h_rep3

description: 100 uM phosphate added_0 h

source_name: Phosphate replete P. ubique str. 7211 time point 0 h rep 3


title: CD001-102-255076

description:
CD001-102-255076
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-102


title: CD001-107-254538

description:
CD001-107-254538
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-107


title: CD001-100-255037

description:
CD001-100-255037
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-100


title: CD001-099-255040

description:
CD001-099-255040
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-099


title: CD001-106-254520

description:
CD001-106-254520
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-106


title: CD001-101-255064

description:
CD001-101-255064
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-101


title: str_7211_noPi_T0h_rep3

description: No phosphate added_0 h

source_name: Phosphate deplete P. ubique str. 7211 time point 0 h rep 3


title: str_7211_+Pi_T0h_rep1

description: 100 uM phosphate added_0 h

source_name: Phosphate replete P. ubique str. 7211 time point 0 h rep 1


title: str_7211_noPi_T0h_rep1

description: No phosphate added_0 h

source_name: Phosphate deplete P. ubique str. 7211 time point 0 h rep 1


title: str_7211_+Pi_T0h_rep2

description: 100 uM phosphate added_0 h

source_name: Phosphate replete P. ubique str. 7211 time point 0 h rep 2


title: str_7211_noPi_T0h_rep2

description: No phosphate added_0 h

source_name: Phosphate deplete P. ubique str. 7211 time point 0 h rep 2


title: str_1062_noPi_T38h_rep2

description: No phosphate added_38 h

source_name: Phosphate deplete P. ubique str. HTCC1062 time point 38 h rep 2


title: str_1062_noPi_T38h_rep1

description: No phosphate added_38 h

source_name: Phosphate deplete P. ubique str. HTCC1062 time point 38 h rep 1


title: str_1062_noPi_T20h_rep3

description: No phosphate added_20 h

source_name: Phosphate deplete P. ubique str. HTCC1062 time point 20 h rep 3


title: CD001-109-254557

description:
CD001-109-254557
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-109

source_name: P. falciparum 3D7 RNA reference pool


title: str_1062_noPi_T20h_rep2

description: No phosphate added_20 h

source_name: Phosphate deplete P. ubique str. HTCC1062 time point 20 h rep 2


title: str_1062_noPi_T4h_rep3

description: No phosphate added_4 h

source_name: Phosphate deplete P. ubique str. HTCC1062 time point 4 h rep 3


title: str_1062_noPi_T20h_rep1

description: No phosphate added_20 h

source_name: Phosphate deplete P. ubique str. HTCC1062 time point 20 h rep 1


title: str_1062_noPi_T4h_rep2

description: No phosphate added_4 h

source_name: Phosphate deplete P. ubique str. HTCC1062 time point 4 h rep 2


title: CD001-097-255006

description:
CD001-097-255006
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-097


title: CD001-094-254989

description:
CD001-094-254989
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-094


title: str_1062_noPi_T0h_rep3

description: No phosphate added_0 h

source_name: Phosphate deplete P. ubique str. HTCC1062 time point 0 h rep 3


title: str_1062_noPi_T4h_rep1

description: No phosphate added_4 h

source_name: Phosphate deplete P. ubique str. HTCC1062 time point 4 h rep 1


title: str_1062_noPi_T0h_rep2

description: No phosphate added_0 h

source_name: Phosphate deplete P. ubique str. HTCC1062 time point 0 h rep 2


title: CD001-095-254991

description:
CD001-095-254991
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-095


title: CD001-093-254971

description:
CD001-093-254971
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-093


title: CD001-096-255010

description:
CD001-096-255010
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-096


title: CD001-088-253612

description:
CD001-088-253612
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-088


title: CD001-092-254968

description:
CD001-092-254968
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-092


title: CD001-086-253572

description:
CD001-086-253572
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-086


title: CD001-085-253569

description:
CD001-085-253569
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-085


title: CD001-084-253546

description:
CD001-084-253546
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-084

source_name: P. falciparum 3D7 RNA reference pool


title: CD001-087-253609

description:
CD001-087-253609
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-087


title: CD001-091-254927

description:
CD001-091-254927
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-091


title: str_1062+Pi_T20h_rep1

description: 100 uM phosphate added_20 h

source_name: Phosphate replete P. ubique str. HTCC1062 time point 20 h rep 1


title: CD001-098-255046

description:
CD001-098-255046
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-098


title: str_1062+Pi_T20h_rep2

description: 100 uM phosphate added_20 h

source_name: Phosphate replete P. ubique str. HTCC1062 time point 20 h rep 2


title: str_1062+Pi_T4h_rep3

description: 100 uM phosphate added_4 h

source_name: Phosphate replete P. ubique str. HTCC1062 time point 4 h rep 3


title: str_1062+Pi_T20h_rep3

description: 100 uM phosphate added_20 h

source_name: Phosphate replete P. ubique str. HTCC1062 time point 20 h rep 3


title: str_1062+Pi_T38h_rep3

description: 100 uM phosphate added_38 h

source_name: Phosphate replete P. ubique str. HTCC1062 time point 38 h rep 3


title: str_1062+Pi_T38h_rep1

description: 100 uM phosphate added_38 h

source_name: Phosphate replete P. ubique str. HTCC1062 time point 38 h rep 1


title: CD001-089-254935

description:
CD001-089-254935
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-089


title: str_1062+Pi_T38h_rep2

description: 100 uM phosphate added_38 h

source_name: Phosphate replete P. ubique str. HTCC1062 time point 38 h rep 2


title: str_1062+Pi_T4h_rep1

description: 100 uM phosphate added_4 h

source_name: Phosphate replete P. ubique str. HTCC1062 time point 4 h rep 1


title: str_1062_noPi_T0h_rep1

description: No phosphate added_0 h

source_name: Phosphate deplete P. ubique str. HTCC1062 time point 0 h rep 1


title: CD001-083-253543

description:
CD001-083-253543
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-083


title: str_1062+Pi_T0h_rep3

description: 100 uM phosphate added_0 h

source_name: Phosphate replete P. ubique str. HTCC1062 time point 0 h rep 3


title: CD001-082-253539

description:
CD001-082-253539
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-082


title: str_1062+Pi_T0h_rep2

description: 100 uM phosphate added_0 h

source_name: Phosphate replete P. ubique str. HTCC1062 time point 0 h rep 2


title: CD001-090-254931

description:
CD001-090-254931
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-090

source_name: P. falciparum 3D7 RNA reference pool


title: str_1062+Pi_T4h_rep2

description: 100 uM phosphate added_4 h

source_name: Phosphate replete P. ubique str. HTCC1062 time point 4 h rep 2


title: str_1062+Pi_T0h_rep1

description: 100 uM phosphate added_0 h

source_name: Phosphate replete P. ubique str. HTCC1062 time point 0 h rep 1


title: CD001-080-253518

description:
CD001-080-253518
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-080


title: CRV versus SG511_replicat 3

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

description: Chitosan resistant CRM

hyb_protocol: A mixture of cDNA obtained from reverse transcription of RNA from WT or mutant strains were diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. Per chip and per spot normalisation wee performed in GeneSpring (7.3)

label: cyanine 3

organism: Staphylococcus aureus

source_name: S. aureus WT strain grown in CAMHB

label_protocol: Incorporation of cyanine dye during reverse transcription

growth_protocol: S. aureus strains were grown in CAMHB (BBL, Becton Dickinson) and extracted at early exponential phase (3h)

extract_protocol: Briefly, bacteria were stabilized in RNA protect for 5 minutes, then harvested. Cells were lysed in the presence of 600 µg/ml lysostaphin and total RNA was extracted using the PrestoSpin R bug Kit including DNase I treatment (Molzym). Quantity and absence of contaminating DNA was measured by using the Nanodrop spectrophotometer (Nanodrop Technologies), and by qPCR, respectively.

treatment_protocol: RNAProtect (Qiagen)

value: SG511 wild type

label: cyanine 5

source_name: S. aureus mutant strain grown in CAMHB

value: spontaneous chitosan resistant variant (CRV)


title: CRV versus SG511_replicat 1

description: Chitosan resistant CRM


title: CRV versus SG511_replicat 2

description: Chitosan resistant CRM


title: CD001-079-253517

description:
CD001-079-253517
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-079


title: CD001-081-253910

description:
CD001-081-253910
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-081


title: CD001-078-253884

description:
CD001-078-253884
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-078


title: CD001-073-253837

description:
CD001-073-253837
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-073


title: CD001-069-253647

description:
CD001-069-253647
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-069


title: CD001-075-253865

description:
CD001-075-253865
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-075


title: CD001-070-253641

description:
CD001-070-253641
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-070


title: CD001-074-253840

description:
CD001-074-253840
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-074


title: CD001-076-253864

description:
CD001-076-253864
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-076


title: CD001-071-253618

description:
CD001-071-253618
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-071


title: CD001-066-253685

description:
CD001-066-253685
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-066


title: CD001-068-253659

description:
CD001-068-253659
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-068

source_name: P. falciparum 3D7 RNA reference pool


title: CD001-072-253621

description:
CD001-072-253621
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-072


title: CD001-064-253691

description:
CD001-064-253691
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-064


title: CD001-063-253448

description:
CD001-063-253448
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-063


title: CCD-34Lu-NP-24+24H-23

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

hyb_protocol: Samples were hybridized to Whole Human Genome Microarray 4 x 44K (G4112F, Agilent Technologies). 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were washed with Agilent Gene Expression wash buffers and Stabilization and Drying Solution as suggest by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) at 100% and 10% sensitivity settings.

data_processing: Only spots with signal minus background flagged as positive and significant (flag=1) were used in the following analysis as “detected” spot while probes with flag equal to 0 were noted as “null”. Probes with less than 83% of detected spots across all arrays were removed from the analysis. Background corrected intensities of replicated spots on each array were averaged. Data were inter-array normalized with Quantile normalization (Bolstad BM et al., Bioinformatics (2003), 19(2):185-93) and then log2-transformed. Cluster analysis and profile similarity searching were performed with tMev that is part of the TM4 Microarray Software Suite (Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, et al. Methods in Enzymology. 2006;411:134-93). Identification of differentially expressed genes was performed with two class Significance Analysis of Microarray (SAM) program (Tusher VG, Tibshirani R, Chu G. Proc Natl Acad Sci USA 2001;98:5116-121) with default settings. SAM uses a permutation-based multiple testing algorithm and identifies significant genes with variable false-discovery rates (FDR). This can be manually adjusted to include a reasonable number of candidate genes with acceptable and well defined error probabilities.

organism: Homo sapiens

source_name: CCD-34Lu cells, treated with PEGylated ORMOSIL nanoparticles (NPs)

label_protocol: 1 microgram of total RNA was labeled with “Agilent One-Color Microarray-Based Gene Expression protocol” (Agilent) according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labelled with cyanine 3-labelled nucleotide. Labeled cRNA was purified with RNeasy Mini columns (Qiagen). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurement (NanoDrop Technologies).

extract_protocol: Total RNA was isolated from 1.5-2 x 106 cells by using Trizol® Reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was quantified using the ND-1000 spectrophotometer (Nanodrop), while RNA integrity was assessed by capillary electrophoresis using the RNA 6000 Nano LabChip using the Agilent Bioanalyzer 2100 (Agilent Technologies). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6, or higher, were used for microarray analysis.

treatment_protocol: 0.5 x 106 cells were plated and maintained  for 24 h in culture medium (10% FBS); then the medium was replaced with F-12K (3% FBS) for additional 24 h.

tag: cell line

tag: cell type

value: normal lung fibroblasts, female, black, 2.5 weeks. Maintained in DMEM medium supplemented with 10% FBS 0.1 mM MEM non essential aminoacids, 0.02 M HEPES.


title: CCD-34Lu-NP-24H-20


title: CCD-34Lu-NP-24H-19


title: CCD-34Lu-CTRL-24+24H-18

source_name: CCD-34Lu cells, untreated


title: CCD-34Lu-NP-24H-21


title: CCD-34Lu-CTRL-24+24H-17


title: CCD-34Lu-CTRL-24+24H-16


title: CCD-34Lu-CTRL-24H-15


title: CD001-062-253476

description:
CD001-062-253476
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-062


title: CD001-061-253481

description:
CD001-061-253481
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-061


title: CCD-34Lu-NP-24+24H-24


title: CCD-34Lu-CTRL-24H-14


title: A549-NP-24+24H-12

source_name: A549 cells, treated with PEGylated ORMOSIL nanoparticles (NPs)

value: lung carcinoma, epithelial, male, 58 years, caucasian. Maintained in F12-K medium supplemented with 10% FBS.


title: CCD-34Lu-NP-24+24H-22


title: CD001-057-253769

description:
CD001-057-253769
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-057


title: CD001-056-253768

description:
CD001-056-253768
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-056


title: CD001-058-253497

description:
CD001-058-253497
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-058


title: CD001-059-253810

description:
CD001-059-253810
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-059


title: CD001-052-228907

description:
CD001-052-228907
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-052


title: CD001-053-228938

description:
CD001-053-228938
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-053


title: CD001-051-228562

description:
CD001-051-228562
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-051


title: A549-NP-24H-9


title: CD001-055-228963

description:
CD001-055-228963
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-055


title: CD001-049-228560

description:
CD001-049-228560
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-049

source_name: P. falciparum 3D7 RNA reference pool


title: A549-CTRL-24+24H-4

source_name: A549 cells, untreated


title: A549-CTRL-24H-2


title: CD001-050-228561

description:
CD001-050-228561
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-050


title: CD001-047-228905

description:
CD001-047-228905
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-047


title: A549-NP-24+24H-10


title: A549-NP-24H-7


title: CD001-065-253687

description:
CD001-065-253687
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-065


title: A549-CTRL-24+24H-5


title: A549-NP-24H-8


title: CD001-077-253863

description:
CD001-077-253863
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-077


title: CD001-046-228659

description:
CD001-046-228659
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-046


title: A549-CTRL-24+24H-6

description: Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.


title: A549-CTRL-24H-3


title: CD001-044-228657

description:
CD001-044-228657
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-044


title: Secretory-stage, Biological rep4

city: Los Angeles

first: Michael

last: Paine

state: CA

address: 2250 Alcazar Street

institute: USC

description:
Gene expression data of secretory-stage enamel organ from rat incisor
S4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit.

value: Wistar

tag: age

tag: tissue

value: secretory-stage incisor enamel organ


title: CD001-045-228658

description:
CD001-045-228658
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-045

value: in vivo


title: A549-CTRL-24H-1


title: A549-NP-24+24H-11

source_name: A549 cells, treated with PEGylated ORMOSIL nanoparticles (NPs)


title: Maturation-stage, Biological rep3

description:
Gene expression data of maturation-stage enamel organ from rat incisor
M3

source_name: secretory-stage enamel organ from rat incisor

value: maturation-stage incisor enamel organ


title: Secretory-stage, Biological rep3

description:
Gene expression data of secretory-stage enamel organ from rat incisor
S3


title: CD001-054-228964

description:
CD001-054-228964
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-054

value: blood


title: CD001-042-228608

description:
CD001-042-228608
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-042

value: prior to artemisinin combination therapy (ACT)


title: CD001-041-228580

description:
CD001-041-228580
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-041

value: In vitro


title: Maturation-stage, Biological rep1

description:
Gene expression data of maturation-stage enamel organ from rat incisor
M1

source_name: marutation-stage enamel organ from rat incisor


title: CD001-040-228578

description:
CD001-040-228578
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-040

value: asexual blood


title: CD001-039-228741

description:
CD001-039-228741
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-039

value: mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle


title: CD001-038-228680

description:
CD001-038-228680
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-038

source_name: P. falciparum 3D7 RNA reference pool

value: reference


title: CD001-033-NOBC

description:
CD001-033-NOBC
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-033


title: CD001-035-NOBC

description:
CD001-035-NOBC
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-035


title: CD001-037-228679

description:
CD001-037-228679
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-037


title: Maturation-stage, Biological rep2

description:
Gene expression data of maturation-stage enamel organ from rat incisor
M2


title: Maturation-stage, Biological rep4

description:
Gene expression data of maturation-stage enamel organ from rat incisor
M4


title: CD001-031-NOBC

description:
CD001-031-NOBC
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-031


title: Secretory-stage, Biological rep1

description:
Gene expression data of secretory-stage enamel organ from rat incisor
S1


title: CD001-030-NOBC

description:
CD001-030-NOBC
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-030


title: CD001-028-211712

description:
CD001-028-211712
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-028


title: CD001-029-211713

description:
CD001-029-211713
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-029


title: CD001-027-211711

description:
CD001-027-211711
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-027


title: CD001-032-NOBC

description:
CD001-032-NOBC
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-032


title: Secretory-stage, Biological rep2

description:
Gene expression data of secretory-stage enamel organ from rat incisor
S2


title: CD001-034-NOBC

description:
CD001-034-NOBC
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-034


title: CD001-025-211671

description:
CD001-025-211671
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-025


title: CD001-036-NOBC

description:
CD001-036-NOBC
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-036


title: CD001-024-231887

description:
CD001-024-231887
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-024


title: CD001-026-211673

description:
CD001-026-211673
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-026


title: CD001-007-211818

description:
CD001-007-211818
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-007


title: CD001-003-211782

description:
CD001-003-211782
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-003


title: CD001-011-211469

description:
CD001-011-211469
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-011

source_name: P. falciparum 3D7 RNA reference pool


title: CD001-006-211802

description:
CD001-006-211802
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-006


title: CD001-023-231888

description:
CD001-023-231888
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-023


title: CD001-013-211483

description:
CD001-013-211483
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-013


title: CD001-019-211257

description:
CD001-019-211257
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-019


title: CD001-008-NOBC

description:
CD001-008-NOBC
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-008


title: CD001-018-211539

description:
CD001-018-211539
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-018


title: CD001-010-211449

description:
CD001-010-211449
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-010


title: BD001-053-231162

description:
BD001-053-231162
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-053

value: Ramu, Bangladesh


title: BD001-054-231175

description:
BD001-054-231175
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-054


title: BD001-055-230877

description:
BD001-055-230877
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-055


title: CD001-014-211499

description:
CD001-014-211499
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-014


title: CD001-021-231856

description:
CD001-021-231856
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-021


title: CD001-002-211756

description:
CD001-002-211756
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-002


title: CD001-016-211532

description:
CD001-016-211532
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-016


title: CD001-017-211536

description:
CD001-017-211536
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-017


title: CD001-012-211468

description:
CD001-012-211468
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-012


title: CD001-005-211786

description:
CD001-005-211786
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-005

source_name: P. falciparum 3D7 RNA reference pool


title: CD001-015-211503

description:
CD001-015-211503
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-015


title: CD001-004-211784

description:
CD001-004-211784
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-004


title: CD001-001-211757

description:
CD001-001-211757
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-001


title: BD001-056-230889

description:
BD001-056-230889
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-056


title: CD001-009-211833

description:
CD001-009-211833
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Kinshasa DRCongo, CD001-009


title: CCD-34Lu-CTRL-24H-13

description: Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

source_name: CCD-34Lu cells, untreated

value: human normal lung fibroblasts, female, black, 2.5 weeks. Maintained in DMEM medium supplemented with 10% FBS 0.1 mM MEM non essential aminoacids, 0.02 M HEPES.


title: BD001-052-230828

description:
BD001-052-230828
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-052


title: BD001-051-230816

description:
BD001-051-230816
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-051


title: BD001-048-230779

description:
BD001-048-230779
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-048


title: BD001-044-230854

description:
BD001-044-230854
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-044


title: BD001-049-230793

description:
BD001-049-230793
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-049


title: BD001-042-219866

description:
BD001-042-219866
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-042


title: BD001-045-230866

description:
BD001-045-230866
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-045


title: BD001-038-231134

description:
BD001-038-231134
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-038


title: BD001-039-231141

description:
BD001-039-231141
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-039


title: BD001-040-219844

description:
BD001-040-219844
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-040


title: BD001-050-230803

description:
BD001-050-230803
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-050

source_name: P. falciparum 3D7 RNA reference pool


title: BD001-041-219855

description:
BD001-041-219855
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-041


title: BD001-037-231116

description:
BD001-037-231116
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-037


title: BD001-034-231080

description:
BD001-034-231080
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-034


title: BD001-032-231035

description:
BD001-032-231035
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-032


title: BD001-043-231148

description:
BD001-043-231148
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-043


title: BD001-030-231011

description:
BD001-030-231011
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-030


title: HfQ3-cy5_WT3-cy3

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description: Biological replicate 3 of 4.

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers.

scan_protocol: Scanned on a GenePix Pro 6 dual-channel laser scanner.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicate : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridioides difficile

source_name: hfQ mutant grown 7.5h Tyt

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with Cy5 or Cy3 dyes 1h at room temperature in the dark.

growth_protocol: C. difficile strain C630E and hfQ mutant were grown in Tyt.

extract_protocol: Total RNA was extracted using QIAgen RNeasy kit.

value: C630E Mullany hfQ::erm

tag: genotype/variation

value: hfQ mutation

source_name: 630E strain grown 7.5h in Tyt (reference)

value: C630E Mullany

value: wild-type


title: HfQ4-cy5_WT4-cy3

description: Biological replicate 4 of 4.


title: BD001-033-231074

description:
BD001-033-231074
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-033


title: BD001-029-231004

description:
BD001-029-231004
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-029


title: HfQ1-cy3_WT1-cy5

description: Biological replicate 1 of 4.


title: BD001-047-230771

description:
BD001-047-230771
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-047


title: BD001-036-231099

description:
BD001-036-231099
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-036


title: BD001-035-231101

description:
BD001-035-231101
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-035


title: BD001-046-230757

description:
BD001-046-230757
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-046


title: BD001-027-230975

description:
BD001-027-230975
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-027


title: BD001-028-230993

description:
BD001-028-230993
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-028


title: BD001-026-231062

description:
BD001-026-231062
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-026

source_name: P. falciparum 3D7 RNA reference pool


title: Muscle_diabetes_7 days after treatment with STZ_biol. rep. 3

description: Gene expression profiling of the gastrocnemius muscle from CD1 diabetic-mice (7 days after treatment with STZ, G6.1)

hyb_protocol: Labeled targets (atrophic and control muscle) were mixed and ethanol precipitated. After dissolving the pellet in 120 µl of hybridization buffer (5X SSC, 0.1% SDS, 25% formamide), samples were denatured at 90°C for 2 min and added to the microarrays. Prehybridization was performed overnight at 48°C in the presence of 5X SSC, 5X Denhardt, 0.1% SDS, 100 ng/µl ss-DNA. Competitive hybridizations were carried on for 48 hours at 46°C in an ArrayBooster microarray incubator (Advalytix), followed by a series of post-hybridization washings (Chemello et al., 2011).

scan_protocol: Array scanning was carried out using a GSI Lumonics LITE dual confocal laser scanner with a ScanArray Microarray Analysis System (Perkin Elmer), and raw images were analyzed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada).

data_processing: Normalization of the expression levels was performed with MIDAW tool (Romualdi et al., 2005 - Nucleic Acids Res. 33: W644-9). Principal component analysis, cluster analysis and profile similarity searching were performed with tMev that is part of the TM4 Microarray Software Suite (Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, et al. Methods in Enzymology, 2006;411:134-93). Identification of differentially expressed genes was performed with one and two class Significance Analysis of Microarray (SAM) program (Tusher VG, Tibshirani R, Chu G. Proc Natl Acad Sci USA 2001;98:5116-121) with default settings. SAM uses a permutation-based multiple testing algorithm and identifies significant genes with variable false-discovery rates (FDR). This can be manually adjusted to include a reasonable number of candidate genes with acceptable and well defined error probabilities

organism: Mus musculus

source_name: Gastrocnemius muscle, control

label_protocol: Total RNA (> 200 nt) samples were labeled using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion), in accordance with the manufacturer's instructions. First strand synthesis with an engineered reverse transcriptase should produce virtually full-length cDNA, which is the best way to ensure reproducible microarray results. The use of a modified oligo(dT) primer bearing a T7 promoter (Van Gelder et al., 1990) allows the next amplification steps: after second strand synthesis and clean-up the cDNA becomes a template for in vitro transcription with T7 RNA polymerase. About 5 µg aminoallyl-labeled aRNA were coupled with Cy5 or Cy3 dyes (GE Healthcare) and purified on column (Ambion).

growth_protocol: Wild-type CD1 mice (Charles River) were housed in a normal environment provided with food and water. All aspects of animal care and experimentation were performed in accordance with the Guide for the Care and Use of Laboratory Animals published by the National Institutes of Health (NIH Publication No. 85-23, Revised 1996) and Italian regulations (DL 116/92) concerning the care and use of laboratory animals. Experimental procedures were approved by the local Ethical Committee of the University of Padova.

extract_protocol: Total RNA was isolated from muscle biopsies by using Trizol® Reagent (Life Technologies, CA) according to the manufacturer’s protocol. Total RNA, enriched for long RNA molecules (> 200 nt) by using PureLink™ miRNA Isolation Kit (Life Technologies), was quantified using the ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), while RNA integrity in each samples were assessed by capillary electrophoresis using the RNA 6000 Nano LabChip using the Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Only total RNA samples with R.I.N. (RNA Integrity Number) values of 6 were used for microarray analysis.

treatment_protocol: CD1 wild-type (wt) mice have been placed under the following muscle wasting conditions: 1) starvation, 2) diabetes and 3) denervation. To confirm the induction of the atrophic process in each condition, we measured in EDL the expression level of Atrogin-1, a muscle specific E3-ubiquitin ligase highly induced during atrophy. 1) To induce muscle wasting by starvation, mice were food deprived for 24 and 48 hours, with free access to water. This procedure reduced body weight by 10%, gastrocnemius muscle mass by 15% and it was accompanied by more than 20 fold increase of Atrogin-1 mRNA. 2) Insulin deficiency or insulin resistance at the level of skeletal muscle tissue also leads to the activation of the atrophic program. In order to recapitulate diabetes-associated muscle atrophy, CD1 wt mice were injected intra-peritoneally with streptozotocin. This drug is recognized and approved by the “Animal Models of Diabetic Complications Consortium” and causes β-cell toxicity, resulting in primary insulin deficiency. After 7 days of an acute injection of 180 mg/Kg of Streptozotocin muscle, atrophy is already established as stated by a 4-5 fold up-regulation of atrogin-1 mRNA. 3) The absence of electrical stimulation and functional load in muscle leads to progressive atrophy. CD1 wt mice underwent sciatic denervation surgery under anaesthesia. The controlateral leg was left intact. Three different time points were analysed: 3, 7 and 14 days after surgery. Three days after surgery expression of Atrogin-1 mRNA was induce by 8–fold when compared to non-denervated muscles.

value: gastrocnemius muscle

tag: treatment

value: control

source_name: Gastrocnemius muscle, diabetes, 7 days after treatment with STZ

value: diabetic

tag: time

value: 7 days after treatment with STZ


title: BD001-024-230956

description:
BD001-024-230956
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-024

tag: culture

value: in vivo

tag: Stage


title: BD001-022-189595

description:
BD001-022-189595
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-022

value: blood

tag: patient sample id

tag: geographic origin


title: BD001-025-231059

description:
BD001-025-231059
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-025

tag: barcode

tag: timepoint

value: prior to artemisinin combination therapy (ACT)


title: BD001-020-219948

description:
BD001-020-219948
Reference sample is laboratory strain 3D7.

source_name: P. falciparum field isolate, Ramu Bangladesh, BD001-020

tag: parasite clearance halflife upon artemisinin treatment (h)

tag: strain/background

value: In vitro