title: ex-vivo_culture_timepoint_2_patient_ID:_M033_2007_Wad Madani_Sudan M033_T2

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP2

value: ex-vivo culture, timepoint 2, M033, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_1315_1994-1996_Kilifi_Kenya 1315_T1

status: Public on Dec 18 2017

type: RNA

first: Margaret

middle: Jane

last: Mackinnon

country: Australia

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning was performed as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v4.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data were excluded if they derived from poor quality spots (regression ratio < 0.6 or flagged by GenePix Pro 6.0 software); probes containing a SNP (based on data from 129 genomes in PlasmoDB); probes matching multiple genes in Version 3 of the 3D7 genome; genes annotated as pseudogenes, var, rif and stevor (i.e., highly variable) genes; and probes with 2-fold or greater differences between the samples and the reference isolate when averaged across all samples (an indication of a deletion or polymorphism in the reference isolate, 336 probes, 45 of which code for genes involved in invasion).

molecule: total RNA

organism: Plasmodium falciparum

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP1

label_protocol: Labeling was carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

growth_protocol: Blood samples from children (3-5ml) were washed and placed in in vitro cultures within 5h of sampling, or were revived from frozen ring-stage parasites, using standard procedures for laboratory culture of P. falciparum.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions.  This was linear amplified for 22 cycles using the SMART protocol as described in Mackinnon, MJ, Li, J, Mok, S, Kortok MM, Marsh, K Preiser, PR, Bozdech, Z..Comparative transcriptional and genomic analysis of Plasmodium falciparum field isolates. PLoS Pathog 2009, 5(10): e1000644.

treatment_protocol: In order to obtain data from all stages of the parasite’s 48h blood stage intraerythrocytic cycle, samples of the culture were taken every 10h for up to 9 times per parasite isolate and processed for RNA extraction.

tag: sample type (culture type,time point,patient id, year, location,country,expt group,expt)

value: ex-vivo culture, timepoint 1, 1315, 1994-1996, Kilifi, Kenya, High, Expt C

source_name: P. falciparum lab-adapted strain P4, mix of samples collected across the 48-hour intraerythrocytic life cycle from synchronised in vitro cultures

tag: sample type (strain,sample type)

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_2_patient_ID:_M035_2007_Wad Madani_Sudan M035_T2

value: ex-vivo culture, timepoint 2, M035, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_1299_1994-1996_Kilifi_Kenya 1299_T2

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP2

value: ex-vivo culture, timepoint 2, 1299, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_M033_2007_Wad Madani_Sudan M033_T1

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP1

value: ex-vivo culture, timepoint 1, M033, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_1354_1994-1996_Kilifi_Kenya 1354_T1

value: ex-vivo culture, timepoint 1, 1354, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1315_1994-1996_Kilifi_Kenya 1315_T2

value: ex-vivo culture, timepoint 2, 1315, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1299_1994-1996_Kilifi_Kenya 1299_T5

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP5

value: ex-vivo culture, timepoint 5, 1299, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_M031_2007_Wad Madani_Sudan M031_T4

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP4

value: ex-vivo culture, timepoint 4, M031, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_0_patient_ID:_1315_1994-1996_Kilifi_Kenya 1315_T0

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP0

value: ex-vivo culture, timepoint 0, 1315, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1299_1994-1996_Kilifi_Kenya 1299_T4

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP4

value: ex-vivo culture, timepoint 4, 1299, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1286_1994-1996_Kilifi_Kenya 1286_T6

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP6

value: ex-vivo culture, timepoint 6, 1286, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1299_1994-1996_Kilifi_Kenya 1299_T3

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP3

value: ex-vivo culture, timepoint 3, 1299, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_M031_2007_Wad Madani_Sudan M031_T3

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP3

value: ex-vivo culture, timepoint 3, M031, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_1286_1994-1996_Kilifi_Kenya 1286_T7

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP7

value: ex-vivo culture, timepoint 7, 1286, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1286_1994-1996_Kilifi_Kenya 1286_T4

value: ex-vivo culture, timepoint 4, 1286, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_M030_2007_Wad Madani_Sudan M030_T4

value: ex-vivo culture, timepoint 4, M030, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_M031_2007_Wad Madani_Sudan M031_T2

value: ex-vivo culture, timepoint 2, M031, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_0_patient_ID:_1286_1994-1996_Kilifi_Kenya 1286_T0

value: ex-vivo culture, timepoint 0, 1286, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_3_patient_ID:_M030_2007_Wad Madani_Sudan M030_T3

value: ex-vivo culture, timepoint 3, M030, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_1212_1994-1996_Kilifi_Kenya 1212_T1

value: ex-vivo culture, timepoint 1, 1212, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1286_1994-1996_Kilifi_Kenya 1286_T3

value: ex-vivo culture, timepoint 3, 1286, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1286_1994-1996_Kilifi_Kenya 1286_T1

value: ex-vivo culture, timepoint 1, 1286, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1212_1994-1996_Kilifi_Kenya 1212_T5

value: ex-vivo culture, timepoint 5, 1212, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_M030_2007_Wad Madani_Sudan M030_T2

value: ex-vivo culture, timepoint 2, M030, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_M030_2007_Wad Madani_Sudan M030_T1

value: ex-vivo culture, timepoint 1, M030, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_1212_1994-1996_Kilifi_Kenya 1212_T7

value: ex-vivo culture, timepoint 7, 1212, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_M025_2007_Wad Madani_Sudan M025_T5

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP5

value: ex-vivo culture, timepoint 5, M025, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_1212_1994-1996_Kilifi_Kenya 1212_T3

value: ex-vivo culture, timepoint 3, 1212, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_M025_2007_Wad Madani_Sudan M025_T4

value: ex-vivo culture, timepoint 4, M025, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_1212_1994-1996_Kilifi_Kenya 1212_T4

value: ex-vivo culture, timepoint 4, 1212, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1180_1994-1996_Kilifi_Kenya 1180_T3

value: ex-vivo culture, timepoint 3, 1180, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1210_1994-1996_Kilifi_Kenya 1210_T1

value: ex-vivo culture, timepoint 1, 1210, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1180_1994-1996_Kilifi_Kenya 1180_T1

value: ex-vivo culture, timepoint 1, 1180, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1212_1994-1996_Kilifi_Kenya 1212_T0

value: ex-vivo culture, timepoint 0, 1212, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1212_1994-1996_Kilifi_Kenya 1212_T2

value: ex-vivo culture, timepoint 2, 1212, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_6_patient_ID:_1096_1994-1996_Kilifi_Kenya 1096_T6

value: ex-vivo culture, timepoint 6, 1096, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_M025_2007_Wad Madani_Sudan M025_T3

value: ex-vivo culture, timepoint 3, M025, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_0_patient_ID:_1210_1994-1996_Kilifi_Kenya 1210_T0

value: ex-vivo culture, timepoint 0, 1210, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_M024_2007_Wad Madani_Sudan M024_T7

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP7

value: ex-vivo culture, timepoint 7, M024, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_1210_1994-1996_Kilifi_Kenya 1210_T7

value: ex-vivo culture, timepoint 7, 1210, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1210_1994-1996_Kilifi_Kenya 1210_T2

value: ex-vivo culture, timepoint 2, 1210, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_M025_2007_Wad Madani_Sudan M025_T1

value: ex-vivo culture, timepoint 1, M025, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_0_patient_ID:_1180_1994-1996_Kilifi_Kenya 1180_T0

value: ex-vivo culture, timepoint 0, 1180, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_M024_2007_Wad Madani_Sudan M024_T6

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP6

value: ex-vivo culture, timepoint 6, M024, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_1078_1994-1996_Kilifi_Kenya 1078_T4

value: ex-vivo culture, timepoint 4, 1078, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_M024_2007_Wad Madani_Sudan M024_T2dup

value: ex-vivo culture, timepoint 2, M024, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_5_patient_ID:_1078_1994-1996_Kilifi_Kenya 1078_T5

value: ex-vivo culture, timepoint 5, 1078, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1096_1994-1996_Kilifi_Kenya 1096_T4

value: ex-vivo culture, timepoint 4, 1096, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_M024_2007_Wad Madani_Sudan M024_T5

value: ex-vivo culture, timepoint 5, M024, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_0_patient_ID:_1096_1994-1996_Kilifi_Kenya 1096_T0

value: ex-vivo culture, timepoint 0, 1096, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_M024_2007_Wad Madani_Sudan M024_T1

value: ex-vivo culture, timepoint 1, M024, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_5_patient_ID:_1077_1994-1996_Kilifi_Kenya 1077_T5

value: ex-vivo culture, timepoint 5, 1077, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_3_patient_ID:_1078_1994-1996_Kilifi_Kenya 1078_T3

value: ex-vivo culture, timepoint 3, 1078, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1078_1994-1996_Kilifi_Kenya 1078_T7

value: ex-vivo culture, timepoint 7, 1078, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1094_1994-1996_Kilifi_Kenya 1094_T6

value: ex-vivo culture, timepoint 6, 1094, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_M024_2007_Wad Madani_Sudan M024_T4

value: ex-vivo culture, timepoint 4, M024, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_M024_2007_Wad Madani_Sudan M024_T2


title: ex-vivo_culture_timepoint_7_patient_ID:_1094_1994-1996_Kilifi_Kenya 1094_T7

value: ex-vivo culture, timepoint 7, 1094, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_M023_2007_Wad Madani_Sudan M023_T6

value: ex-vivo culture, timepoint 6, M023, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_1077_1994-1996_Kilifi_Kenya 1077_T4

value: ex-vivo culture, timepoint 4, 1077, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_M024_2007_Wad Madani_Sudan M024_T1dup


title: ex-vivo_culture_timepoint_4_patient_ID:_1034_1994-1996_Kilifi_Kenya 1034_T4

value: ex-vivo culture, timepoint 4, 1034, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1034_1994-1996_Kilifi_Kenya 1034_T5

value: ex-vivo culture, timepoint 5, 1034, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1078_1994-1996_Kilifi_Kenya 1078_T1

value: ex-vivo culture, timepoint 1, 1078, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1078_1994-1996_Kilifi_Kenya 1078_T0

value: ex-vivo culture, timepoint 0, 1078, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1094_1994-1996_Kilifi_Kenya 1094_T2

value: ex-vivo culture, timepoint 2, 1094, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1078_1994-1996_Kilifi_Kenya 1078_T2

value: ex-vivo culture, timepoint 2, 1078, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_M024_2007_Wad Madani_Sudan M024_T3

value: ex-vivo culture, timepoint 3, M024, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_1034_1994-1996_Kilifi_Kenya 1034_T1

value: ex-vivo culture, timepoint 1, 1034, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1077_1994-1996_Kilifi_Kenya 1077_T0

value: ex-vivo culture, timepoint 0, 1077, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1034_1994-1996_Kilifi_Kenya 1034_T2

value: ex-vivo culture, timepoint 2, 1034, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_7_patient_ID:_M023_2007_Wad Madani_Sudan M023_T7

value: ex-vivo culture, timepoint 7, M023, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_1034_1994-1996_Kilifi_Kenya 1034_T3

value: ex-vivo culture, timepoint 3, 1034, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_M023_2007_Wad Madani_Sudan M023_T2

value: ex-vivo culture, timepoint 2, M023, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_M023_2007_Wad Madani_Sudan M023_T4

value: ex-vivo culture, timepoint 4, M023, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_0_patient_ID:_1034_1994-1996_Kilifi_Kenya 1034_T0

value: ex-vivo culture, timepoint 0, 1034, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1077_1994-1996_Kilifi_Kenya 1077_T7

value: ex-vivo culture, timepoint 7, 1077, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1034_1994-1996_Kilifi_Kenya 1034_T6

value: ex-vivo culture, timepoint 6, 1034, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_M023_2007_Wad Madani_Sudan M023_T1

value: ex-vivo culture, timepoint 1, M023, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_1014_1994-1996_Kilifi_Kenya 1014_T1

value: ex-vivo culture, timepoint 1, 1014, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_M022_2007_Wad Madani_Sudan M022_T7

value: ex-vivo culture, timepoint 7, M022, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_1014_1994-1996_Kilifi_Kenya 1014_T4

value: ex-vivo culture, timepoint 4, 1014, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1014_1994-1996_Kilifi_Kenya 1014_T3

value: ex-vivo culture, timepoint 3, 1014, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1014_1994-1996_Kilifi_Kenya 1014_T6

value: ex-vivo culture, timepoint 6, 1014, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_M022_2007_Wad Madani_Sudan M022_T6

value: ex-vivo culture, timepoint 6, M022, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_M019_2007_Wad Madani_Sudan M019_T7

value: ex-vivo culture, timepoint 7, M019, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_1014_1994-1996_Kilifi_Kenya 1014_T7

value: ex-vivo culture, timepoint 7, 1014, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_Fresh10614_2010-2012_Kilifi_Kenya F10614_T5

value: ex-vivo culture, timepoint 5, Fresh10614, 2010-2012, Kilifi, Kenya, Low, Expt A

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_5_patient_ID:_M022_2007_Wad Madani_Sudan M022_T5

value: ex-vivo culture, timepoint 5, M022, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_M022_2007_Wad Madani_Sudan M022_T2dup

value: ex-vivo culture, timepoint 2, M022, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_0_patient_ID:_1014_1994-1996_Kilifi_Kenya 1014_T0

value: ex-vivo culture, timepoint 0, 1014, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_M022_2007_Wad Madani_Sudan M022_T2


title: InVivoLiver_11w_CKOHFD

city: Gwangju

first: Joo Young

last: Huh

address: 77 Yongbong-ro

department: College of Pharmacy

country: South Korea

institute: Chonnam National University

description:
4
Gene expression after 11 weeks in high fat diet-fed catalase knockout mouse liver.

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Mouse Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: Data was extracted using GeneSpring GX 7.3 (Agilent Technology, USA). Raw intensity data was globally normalized (Cheadle et al.(2003).

organism: Mus musculus

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: All mice were housed under a 12 h light-12 h dark cycle at 20-22°C and had ad libitum access to water during the entire experiment.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: Catalase knockout mice and wild type mice were fed either a normal diet (ND; 18% fat-derived calories) or a high-fat diet (HFD; 60.3% fat-derived calories) from 29 to 40 weeks of age.

tag: genotype/variation

value: catalase knockout

tag: tissue

value: liver

tag: gender

value: male

tag: treatment

value: high-fat diet


title: InVivoLiver_11w_ND

description:
1
Gene expression after 11 weeks in normal diet-fed wild type mouse liver.

value: wild type

value: normal diet


title: ex-vivo_culture_timepoint_3_patient_ID:_Fresh10739_2010-2012_Kilifi_Kenya F10739_T3

value: ex-vivo culture, timepoint 3, Fresh10739, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_Fresh10614_2010-2012_Kilifi_Kenya F10614_T1

value: ex-vivo culture, timepoint 1, Fresh10614, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_Fresh10779_2010-2012_Kilifi_Kenya F10779_T2

value: ex-vivo culture, timepoint 2, Fresh10779, 2010-2012, Kilifi, Kenya, Low, Expt A


title: InVivoLiver_11w_HFD

description:
2
Gene expression after 11 weeks in high fat diet-fed wild type mouse liver.


title: ex-vivo_culture_timepoint_3_patient_ID:_Fresh10614_2010-2012_Kilifi_Kenya F10614_T3

value: ex-vivo culture, timepoint 3, Fresh10614, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_Fresh10615_2010-2012_Kilifi_Kenya F10615_T1

value: ex-vivo culture, timepoint 1, Fresh10615, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_M019_2007_Wad Madani_Sudan M019_T6

value: ex-vivo culture, timepoint 6, M019, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_5_patient_ID:_M019_2007_Wad Madani_Sudan M019_T5

value: ex-vivo culture, timepoint 5, M019, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_Fresh10614_2010-2012_Kilifi_Kenya F10614_T7

value: ex-vivo culture, timepoint 7, Fresh10614, 2010-2012, Kilifi, Kenya, Low, Expt A

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_2_patient_ID:_Fresh10614_2010-2012_Kilifi_Kenya F10614_T2

value: ex-vivo culture, timepoint 2, Fresh10614, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_10612_2010-2012_Kilifi_Kenya F10612_T6

value: ex-vivo culture, timepoint 6, 10612, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_10612_2010-2012_Kilifi_Kenya F10612_T4

value: ex-vivo culture, timepoint 4, 10612, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_10612_2010-2012_Kilifi_Kenya F10612_T1

value: ex-vivo culture, timepoint 1, 10612, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_M019_2007_Wad Madani_Sudan M019_T3

value: ex-vivo culture, timepoint 3, M019, 2007, Wad Madani, Sudan, Low, Expt B


title: InVivoLiver_11w_CKOND

description:
3
Gene expression after 11 weeks in normal diet-fed catalase knockout mouse liver.

value: catalase knockout

value: liver

value: male


title: ex-vivo_culture_timepoint_6_patient_ID:_10595_2010-2012_Kilifi_Kenya F10595_T6

value: ex-vivo culture, timepoint 6, 10595, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_M019_2007_Wad Madani_Sudan M019_T4

value: ex-vivo culture, timepoint 4, M019, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_M022_2007_Wad Madani_Sudan M022_T1

value: ex-vivo culture, timepoint 1, M022, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_10612_2010-2012_Kilifi_Kenya F10612_T2

value: ex-vivo culture, timepoint 2, 10612, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_10595_2010-2012_Kilifi_Kenya F10595_T7

value: ex-vivo culture, timepoint 7, 10595, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_10595_2010-2012_Kilifi_Kenya F10595_T5

value: ex-vivo culture, timepoint 5, 10595, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_10595_2010-2012_Kilifi_Kenya F10595_T3

value: ex-vivo culture, timepoint 3, 10595, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_10595_2010-2012_Kilifi_Kenya F10595_T4

value: ex-vivo culture, timepoint 4, 10595, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_M018_2007_Wad Madani_Sudan M018_T5

value: ex-vivo culture, timepoint 5, M018, 2007, Wad Madani, Sudan, Low, Expt B

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_1_patient_ID:_Fresh10761_2010-2012_Kilifi_Kenya F10761_T1

value: ex-vivo culture, timepoint 1, Fresh10761, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_10595_2010-2012_Kilifi_Kenya F10595_T2

value: ex-vivo culture, timepoint 2, 10595, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_10595_2010-2012_Kilifi_Kenya F10595_T1

value: ex-vivo culture, timepoint 1, 10595, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_M018_2007_Wad Madani_Sudan M018_T4

value: ex-vivo culture, timepoint 4, M018, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_M018_2007_Wad Madani_Sudan M018_T1

value: ex-vivo culture, timepoint 1, M018, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_6_patient_ID:_10594_2010-2012_Kilifi_Kenya F10594_T6

value: ex-vivo culture, timepoint 6, 10594, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_10594_2010-2012_Kilifi_Kenya F10594_T3

value: ex-vivo culture, timepoint 3, 10594, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_10594_2010-2012_Kilifi_Kenya F10594_T5

value: ex-vivo culture, timepoint 5, 10594, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_10594_2010-2012_Kilifi_Kenya F10594_T7

value: ex-vivo culture, timepoint 7, 10594, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_M015_2007_Wad Madani_Sudan M015_T7

value: ex-vivo culture, timepoint 7, M015, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_M018_2007_Wad Madani_Sudan M018_T7

value: ex-vivo culture, timepoint 7, M018, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_10593_2010-2012_Kilifi_Kenya F10593_T7

value: ex-vivo culture, timepoint 7, 10593, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_M015_2007_Wad Madani_Sudan M015_T6

value: ex-vivo culture, timepoint 6, M015, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_5_patient_ID:_M015_2007_Wad Madani_Sudan M015_T5

value: ex-vivo culture, timepoint 5, M015, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_10594_2010-2012_Kilifi_Kenya F10594_T2

value: ex-vivo culture, timepoint 2, 10594, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_10594_2010-2012_Kilifi_Kenya F10594_T1

value: ex-vivo culture, timepoint 1, 10594, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_10593_2010-2012_Kilifi_Kenya F10593_T5

value: ex-vivo culture, timepoint 5, 10593, 2010-2012, Kilifi, Kenya, Low, Expt A

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_4_patient_ID:_10594_2010-2012_Kilifi_Kenya F10594_T4

value: ex-vivo culture, timepoint 4, 10594, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_M015_2007_Wad Madani_Sudan M015_T4

value: ex-vivo culture, timepoint 4, M015, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_6_patient_ID:_10593_2010-2012_Kilifi_Kenya F10593_T6

value: ex-vivo culture, timepoint 6, 10593, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_10593_2010-2012_Kilifi_Kenya F10593_T3

value: ex-vivo culture, timepoint 3, 10593, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_K0071_2008_Kisumu_Kenya K0071_T6

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP6

value: ex-vivo culture, timepoint 6, K0071, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_M015_2007_Wad Madani_Sudan M015_T1

value: ex-vivo culture, timepoint 1, M015, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_M015_2007_Wad Madani_Sudan M015_T2

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP2

value: ex-vivo culture, timepoint 2, M015, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_6_patient_ID:_M014_2007_Wad Madani_Sudan M014_T6

value: ex-vivo culture, timepoint 6, M014, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_10593_2010-2012_Kilifi_Kenya F10593_T4

value: ex-vivo culture, timepoint 4, 10593, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_K0068_2008_Kisumu_Kenya K0068_T7

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP7

value: ex-vivo culture, timepoint 7, K0068, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_K0068_2008_Kisumu_Kenya K0068_T3

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP3

value: ex-vivo culture, timepoint 3, K0068, 2008, Kisumu, Kenya, High, Expt A

source_name: P. falciparum lab-adapted strain P4, mix of samples collected across the 48-hour intraerythrocytic life cycle from synchronised in vitro cultures


title: ex-vivo_culture_timepoint_2_patient_ID:_K0068_2008_Kisumu_Kenya K0068_T2

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP2

value: ex-vivo culture, timepoint 2, K0068, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_K0071_2008_Kisumu_Kenya K0071_T1

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP1

value: ex-vivo culture, timepoint 1, K0071, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_10593_2010-2012_Kilifi_Kenya F10593_T1

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP1

value: ex-vivo culture, timepoint 1, 10593, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_K0068_2008_Kisumu_Kenya K0068_T6

value: ex-vivo culture, timepoint 6, K0068, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_10612_2010-2012_Kilifi_Kenya F10612_T3

value: ex-vivo culture, timepoint 3, 10612, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_M014_2007_Wad Madani_Sudan M014_T1

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP1

value: ex-vivo culture, timepoint 1, M014, 2007, Wad Madani, Sudan, Low, Expt B

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_5_patient_ID:_10612_2010-2012_Kilifi_Kenya F10612_T5

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP5

value: ex-vivo culture, timepoint 5, 10612, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_M014_2007_Wad Madani_Sudan M014_T4

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP4

value: ex-vivo culture, timepoint 4, M014, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_M015_2007_Wad Madani_Sudan M015_T3

value: ex-vivo culture, timepoint 3, M015, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_5_patient_ID:_K0068_2008_Kisumu_Kenya K0068_T5

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP5

value: ex-vivo culture, timepoint 5, K0068, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_K0067_2008_Kisumu_Kenya K0067_T2

value: ex-vivo culture, timepoint 2, K0067, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_M014_2007_Wad Madani_Sudan M014_T2

value: ex-vivo culture, timepoint 2, M014, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_5_patient_ID:_M014_2007_Wad Madani_Sudan M014_T5

value: ex-vivo culture, timepoint 5, M014, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_K0067_2008_Kisumu_Kenya K0067_T7

value: ex-vivo culture, timepoint 7, K0067, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_K0066_2008_Kisumu_Kenya K0066_T2

value: ex-vivo culture, timepoint 2, K0066, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_K0066_2008_Kisumu_Kenya K0066_T5

value: ex-vivo culture, timepoint 5, K0066, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_K0066_2008_Kisumu_Kenya K0066_T6

value: ex-vivo culture, timepoint 6, K0066, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_K0068_2008_Kisumu_Kenya K0068_T4

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP4

value: ex-vivo culture, timepoint 4, K0068, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_K0066_2008_Kisumu_Kenya K0066_T1

value: ex-vivo culture, timepoint 1, K0066, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_M013_2007_Wad Madani_Sudan M013_T2

value: ex-vivo culture, timepoint 2, M013, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_K0066_2008_Kisumu_Kenya K0066_T4

value: ex-vivo culture, timepoint 4, K0066, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_M012_2007_Wad Madani_Sudan M012_T7

value: ex-vivo culture, timepoint 7, M012, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_K0066_2008_Kisumu_Kenya K0066_T3

value: ex-vivo culture, timepoint 3, K0066, 2008, Kisumu, Kenya, High, Expt A

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_5_patient_ID:_M013_2007_Wad Madani_Sudan M013_T5

value: ex-vivo culture, timepoint 5, M013, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_K0067_2008_Kisumu_Kenya K0067_T4

value: ex-vivo culture, timepoint 4, K0067, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_10593_2010-2012_Kilifi_Kenya F10593_T2

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP2

value: ex-vivo culture, timepoint 2, 10593, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_M012_2007_Wad Madani_Sudan M012_T6

value: ex-vivo culture, timepoint 6, M012, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_K0065_2008_Kisumu_Kenya K0065_T2

value: ex-vivo culture, timepoint 2, K0065, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_K0065_2008_Kisumu_Kenya K0065_T5

value: ex-vivo culture, timepoint 5, K0065, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_M012_2007_Wad Madani_Sudan M012_T2

value: ex-vivo culture, timepoint 2, M012, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_6_patient_ID:_K0065_2008_Kisumu_Kenya K0065_T6

value: ex-vivo culture, timepoint 6, K0065, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_K0065_2008_Kisumu_Kenya K0065_T4

value: ex-vivo culture, timepoint 4, K0065, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_K0065_2008_Kisumu_Kenya K0065_T1

value: ex-vivo culture, timepoint 1, K0065, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_K0067_2008_Kisumu_Kenya K0067_T6

value: ex-vivo culture, timepoint 6, K0067, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_K0064_2008_Kisumu_Kenya K0064_T2

value: ex-vivo culture, timepoint 2, K0064, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_8_patient_ID:_M011_2007_Wad Madani_Sudan M011_T8

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP8

value: ex-vivo culture, timepoint 8, M011, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_K0063_2008_Kisumu_Kenya K0063_T3

value: ex-vivo culture, timepoint 3, K0063, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_M011_2007_Wad Madani_Sudan M011_T6

value: ex-vivo culture, timepoint 6, M011, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_M011_2007_Wad Madani_Sudan M011_T7

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP7

value: ex-vivo culture, timepoint 7, M011, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_M012_2007_Wad Madani_Sudan M012_T1

value: ex-vivo culture, timepoint 1, M012, 2007, Wad Madani, Sudan, Low, Expt B

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_5_patient_ID:_M011_2007_Wad Madani_Sudan M011_T5

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP5

value: ex-vivo culture, timepoint 5, M011, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_K0064_2008_Kisumu_Kenya K0064_T4

value: ex-vivo culture, timepoint 4, K0064, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_K0063_2008_Kisumu_Kenya K0063_T5

value: ex-vivo culture, timepoint 5, K0063, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_K0063_2008_Kisumu_Kenya K0063_T7

value: ex-vivo culture, timepoint 7, K0063, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_8_patient_ID:_M009_2007_Wad Madani_Sudan M009_T8

value: ex-vivo culture, timepoint 8, M009, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_K0024_2008_Kisumu_Kenya K0024_T2

value: ex-vivo culture, timepoint 2, K0024, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_K0024_2008_Kisumu_Kenya K0024_T6

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP6

value: ex-vivo culture, timepoint 6, K0024, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_K0039_2008_Kisumu_Kenya K0039_T2

value: ex-vivo culture, timepoint 2, K0039, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_K0024_2008_Kisumu_Kenya K0024_T1

value: ex-vivo culture, timepoint 1, K0024, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_K0024_2008_Kisumu_Kenya K0024_T5

value: ex-vivo culture, timepoint 5, K0024, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_K0063_2008_Kisumu_Kenya K0063_T2

value: ex-vivo culture, timepoint 2, K0063, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_K0024_2008_Kisumu_Kenya K0024_T3

value: ex-vivo culture, timepoint 3, K0024, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_M011_2007_Wad Madani_Sudan M011_T2

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP2

value: ex-vivo culture, timepoint 2, M011, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_K0036_2008_Kisumu_Kenya K0036_T3

value: ex-vivo culture, timepoint 3, K0036, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_M011_2007_Wad Madani_Sudan M011_T3

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP3

value: ex-vivo culture, timepoint 3, M011, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_K0008_2008_Kisumu_Kenya K0008_T3

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP3

value: ex-vivo culture, timepoint 3, K0008, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_K0024_2008_Kisumu_Kenya K0024_T7

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP7

value: ex-vivo culture, timepoint 7, K0024, 2008, Kisumu, Kenya, High, Expt A

source_name: P. falciparum lab-adapted strain P4, mix of samples collected across the 48-hour intraerythrocytic life cycle from synchronised in vitro cultures

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_3_patient_ID:_K0010_2008_Kisumu_Kenya K0010_T3

value: ex-vivo culture, timepoint 3, K0010, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_Fresh10820_2010-2012_Kilifi_Kenya F10820_T7

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP7

value: ex-vivo culture, timepoint 7, Fresh10820, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_K0008_2008_Kisumu_Kenya K0008_T6

value: ex-vivo culture, timepoint 6, K0008, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_M009_2007_Wad Madani_Sudan M009_T4

value: ex-vivo culture, timepoint 4, M009, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_5_patient_ID:_M009_2007_Wad Madani_Sudan M009_T5

value: ex-vivo culture, timepoint 5, M009, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_K0024_2008_Kisumu_Kenya K0024_T4

value: ex-vivo culture, timepoint 4, K0024, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_M009_2007_Wad Madani_Sudan M009_T7

value: ex-vivo culture, timepoint 7, M009, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_Fresh10820_2010-2012_Kilifi_Kenya F10820_T4

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP4

value: ex-vivo culture, timepoint 4, Fresh10820, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_Fresh10820_2010-2012_Kilifi_Kenya F10820_T5

value: ex-vivo culture, timepoint 5, Fresh10820, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_M009_2007_Wad Madani_Sudan M009_T3

value: ex-vivo culture, timepoint 3, M009, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_K0008_2008_Kisumu_Kenya K0008_T1

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP1

value: ex-vivo culture, timepoint 1, K0008, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_Fresh10820_2010-2012_Kilifi_Kenya F10820_T1

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP1

value: ex-vivo culture, timepoint 1, Fresh10820, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_Fresh10814_2010-2012_Kilifi_Kenya F10814_T7

value: ex-vivo culture, timepoint 7, Fresh10814, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_M008_2007_Wad Madani_Sudan M008_T5

value: ex-vivo culture, timepoint 5, M008, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_K0008_2008_Kisumu_Kenya K0008_T2

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP2

value: ex-vivo culture, timepoint 2, K0008, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_K0008_2008_Kisumu_Kenya K0008_T4

value: ex-vivo culture, timepoint 4, K0008, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_M008_2007_Wad Madani_Sudan M008_T7

value: ex-vivo culture, timepoint 7, M008, 2007, Wad Madani, Sudan, Low, Expt B

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_6_patient_ID:_Fresh10814_2010-2012_Kilifi_Kenya F10814_T6

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP6

value: ex-vivo culture, timepoint 6, Fresh10814, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_M008_2007_Wad Madani_Sudan M008_T4

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP4

value: ex-vivo culture, timepoint 4, M008, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_Fresh10814_2010-2012_Kilifi_Kenya F10814_T4

value: ex-vivo culture, timepoint 4, Fresh10814, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_K0008_2008_Kisumu_Kenya K0008_T5

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP5

value: ex-vivo culture, timepoint 5, K0008, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_M009_2007_Wad Madani_Sudan M009_T1

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP1

value: ex-vivo culture, timepoint 1, M009, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_Fresh10820_2010-2012_Kilifi_Kenya F10820_T3

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP3

value: ex-vivo culture, timepoint 3, Fresh10820, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_Fresh10814_2010-2012_Kilifi_Kenya F10814_T1

value: ex-vivo culture, timepoint 1, Fresh10814, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_Fresh10814_2010-2012_Kilifi_Kenya F10814_T3

value: ex-vivo culture, timepoint 3, Fresh10814, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_K0017_2008_Kisumu_Kenya K0017_T1

value: ex-vivo culture, timepoint 1, K0017, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_Fresh10814_2010-2012_Kilifi_Kenya F10814_T5

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP5

value: ex-vivo culture, timepoint 5, Fresh10814, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_Fresh10814_2010-2012_Kilifi_Kenya F10814_T2

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP2

value: ex-vivo culture, timepoint 2, Fresh10814, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_M009_2007_Wad Madani_Sudan M009_T2

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP2

value: ex-vivo culture, timepoint 2, M009, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_Fresh10820_2010-2012_Kilifi_Kenya F10820_T2

value: ex-vivo culture, timepoint 2, Fresh10820, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_Fresh10779_2010-2012_Kilifi_Kenya F10779_T3

value: ex-vivo culture, timepoint 3, Fresh10779, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_M007_2007_Wad Madani_Sudan M007_T5

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP5

value: ex-vivo culture, timepoint 5, M007, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_Fresh10761_2010-2012_Kilifi_Kenya F10761_T3

value: ex-vivo culture, timepoint 3, Fresh10761, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_Fresh10761_2010-2012_Kilifi_Kenya F10761_T5

value: ex-vivo culture, timepoint 5, Fresh10761, 2010-2012, Kilifi, Kenya, Low, Expt A

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_5_patient_ID:_Fresh10779_2010-2012_Kilifi_Kenya F10779_T5

value: ex-vivo culture, timepoint 5, Fresh10779, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_Fresh10761_2010-2012_Kilifi_Kenya F10761_T4

value: ex-vivo culture, timepoint 4, Fresh10761, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_Fresh10761_2010-2012_Kilifi_Kenya F10761_T6

value: ex-vivo culture, timepoint 6, Fresh10761, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_M007_2007_Wad Madani_Sudan M007_T2

value: ex-vivo culture, timepoint 2, M007, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_8_patient_ID:_M007_2007_Wad Madani_Sudan M007_T8

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP8

value: ex-vivo culture, timepoint 8, M007, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_Fresh10779_2010-2012_Kilifi_Kenya F10779_T1

value: ex-vivo culture, timepoint 1, Fresh10779, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_8_patient_ID:_M005_2007_Wad Madani_Sudan M005_T8

value: ex-vivo culture, timepoint 8, M005, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_M007_2007_Wad Madani_Sudan M007_T1

value: ex-vivo culture, timepoint 1, M007, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_M008_2007_Wad Madani_Sudan M008_T3

source_name: P. falciparum (ex vivo), Wad Madani, Sudan, TP3

value: ex-vivo culture, timepoint 3, M008, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_5_patient_ID:_K0071_2008_Kisumu_Kenya K0071_T5

value: ex-vivo culture, timepoint 5, K0071, 2008, Kisumu, Kenya, High, Expt A

source_name: P. falciparum lab-adapted strain P4, mix of samples collected across the 48-hour intraerythrocytic life cycle from synchronised in vitro cultures


title: ex-vivo_culture_timepoint_2_patient_ID:_Fresh10615_2010-2012_Kilifi_Kenya F10615_T2

value: ex-vivo culture, timepoint 2, Fresh10615, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_Fresh10615_2010-2012_Kilifi_Kenya F10615_T3

value: ex-vivo culture, timepoint 3, Fresh10615, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_Fresh10615_2010-2012_Kilifi_Kenya F10615_T4

value: ex-vivo culture, timepoint 4, Fresh10615, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_Fresh10615_2010-2012_Kilifi_Kenya F10615_T7

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP7

value: ex-vivo culture, timepoint 7, Fresh10615, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_Fresh10761_2010-2012_Kilifi_Kenya F10761_T2

value: ex-vivo culture, timepoint 2, Fresh10761, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_M005_2007_Wad Madani_Sudan M005_T5

value: ex-vivo culture, timepoint 5, M005, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_M005_2007_Wad Madani_Sudan M005_T3

value: ex-vivo culture, timepoint 3, M005, 2007, Wad Madani, Sudan, Low, Expt B

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_2_patient_ID:_K0071_2008_Kisumu_Kenya K0071_T2

value: ex-vivo culture, timepoint 2, K0071, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_K0071_2008_Kisumu_Kenya K0071_T3

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP3

value: ex-vivo culture, timepoint 3, K0071, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_K0039_2008_Kisumu_Kenya K0039_T3

value: ex-vivo culture, timepoint 3, K0039, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_10612_2010-2012_Kilifi_Kenya F10612_T7

value: ex-vivo culture, timepoint 7, 10612, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_M005_2007_Wad Madani_Sudan M005_T1

value: ex-vivo culture, timepoint 1, M005, 2007, Wad Madani, Sudan, Low, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_R903_2010-2012_Kilifi_Kenya R903_T3

value: ex-vivo culture, timepoint 3, R903, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_R903_2010-2012_Kilifi_Kenya R903_T2

value: ex-vivo culture, timepoint 2, R903, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_K0036_2008_Kisumu_Kenya K0036_T7

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP7

value: ex-vivo culture, timepoint 7, K0036, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_R903_2010-2012_Kilifi_Kenya R903_T5

value: ex-vivo culture, timepoint 5, R903, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_K0036_2008_Kisumu_Kenya K0036_T2

value: ex-vivo culture, timepoint 2, K0036, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_K0039_2008_Kisumu_Kenya K0039_T6

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP6

value: ex-vivo culture, timepoint 6, K0039, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_J787/0_2010-2012_Kilifi_Kenya J787/0_T4

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP4

value: ex-vivo culture, timepoint 4, J787/0, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_6_patient_ID:_K0017_2008_Kisumu_Kenya K0017_T6

value: ex-vivo culture, timepoint 6, K0017, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_K0017_2008_Kisumu_Kenya K0017_T2

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP2

value: ex-vivo culture, timepoint 2, K0017, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_6_patient_ID:_K0010_2008_Kisumu_Kenya K0010_T6

value: ex-vivo culture, timepoint 6, K0010, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_K0039_2008_Kisumu_Kenya K0039_T1

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP1

value: ex-vivo culture, timepoint 1, K0039, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_K0039_2008_Kisumu_Kenya K0039_T5

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP5

value: ex-vivo culture, timepoint 5, K0039, 2008, Kisumu, Kenya, High, Expt A

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_1_patient_ID:_J787/0_2010-2012_Kilifi_Kenya J787/0_T1

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP1

value: ex-vivo culture, timepoint 1, J787/0, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_5_patient_ID:_K0010_2008_Kisumu_Kenya K0010_T5

value: ex-vivo culture, timepoint 5, K0010, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_K0017_2008_Kisumu_Kenya K0017_T3

value: ex-vivo culture, timepoint 3, K0017, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_K0039_2008_Kisumu_Kenya K0039_T4

source_name: P. falciparum (ex vivo), Kisumu, Kenya, TP4

value: ex-vivo culture, timepoint 4, K0039, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_K0039_2008_Kisumu_Kenya K0039_T7

value: ex-vivo culture, timepoint 7, K0039, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_K0010_2008_Kisumu_Kenya K0010_T2

value: ex-vivo culture, timepoint 2, K0010, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_Fresh10615_2010-2012_Kilifi_Kenya F10615_T5

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP5

value: ex-vivo culture, timepoint 5, Fresh10615, 2010-2012, Kilifi, Kenya, Low, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_K0010_2008_Kisumu_Kenya K0010_T1

value: ex-vivo culture, timepoint 1, K0010, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_K0010_2008_Kisumu_Kenya K0010_T7

value: ex-vivo culture, timepoint 7, K0010, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_R903_2010-2012_Kilifi_Kenya R903_T4

value: ex-vivo culture, timepoint 4, R903, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_K0036_2008_Kisumu_Kenya K0036_T1

value: ex-vivo culture, timepoint 1, K0036, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_12298_2010-2012_Kilifi_Kenya 12298_T3

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP3

value: ex-vivo culture, timepoint 3, 12298, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_6_patient_ID:_K0036_2008_Kisumu_Kenya K0036_T6

value: ex-vivo culture, timepoint 6, K0036, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_12298_2010-2012_Kilifi_Kenya 12298_T2

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP2

value: ex-vivo culture, timepoint 2, 12298, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_K0017_2008_Kisumu_Kenya K0017_T4

value: ex-vivo culture, timepoint 4, K0017, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_7_patient_ID:_K0007_2008_Kisumu_Kenya K0007_T7

value: ex-vivo culture, timepoint 7, K0007, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_R903_2010-2012_Kilifi_Kenya R903_T1

value: ex-vivo culture, timepoint 1, R903, 2010-2012, Kilifi, Kenya, High, Expt B

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_2_patient_ID:_K0007_2008_Kisumu_Kenya K0007_T2

value: ex-vivo culture, timepoint 2, K0007, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_K0007_2008_Kisumu_Kenya K0007_T3

value: ex-vivo culture, timepoint 3, K0007, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_K0036_2008_Kisumu_Kenya K0036_T4

value: ex-vivo culture, timepoint 4, K0036, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_1_patient_ID:_K0007_2008_Kisumu_Kenya K0007_T1

value: ex-vivo culture, timepoint 1, K0007, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_K0007_2008_Kisumu_Kenya K0007_T4

value: ex-vivo culture, timepoint 4, K0007, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_4_patient_ID:_12182_2010-2012_Kilifi_Kenya 12182_T4

value: ex-vivo culture, timepoint 4, 12182, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_K0017_2008_Kisumu_Kenya K0017_T7

value: ex-vivo culture, timepoint 7, K0017, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_5_patient_ID:_12182_2010-2012_Kilifi_Kenya 12182_T5

value: ex-vivo culture, timepoint 5, 12182, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_5_patient_ID:_12298_2010-2012_Kilifi_Kenya 12298_T5

value: ex-vivo culture, timepoint 5, 12298, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_2_patient_ID:_J787/0_2010-2012_Kilifi_Kenya J787/0_T2

value: ex-vivo culture, timepoint 2, J787/0, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_5_patient_ID:_J787/0_2010-2012_Kilifi_Kenya J787/0_T5

value: ex-vivo culture, timepoint 5, J787/0, 2010-2012, Kilifi, Kenya, High, Expt B


title: MCM1DLN + PBA, sample 1 [experiment 1, biological replicate 1]

city: Vienna

first: Clemens

last: Röhrl

address: Währingerstraße 10

department: Department of Medical Chemistry

country: Austria

institute: Medical University of Vienna

description: metastatic melanoma cells, treated with 4-PBA

hyb_protocol: fragmented cRNA was hybridized for 16 h at 45°C

scan_protocol: Hewlett-Packard GeneArray Scanner G2500A

data_processing:
Raw data were processed with a well-established pipeline [1] that includes pre-processing, normalization, summarization and filtering. Concretely, quantile-normalization [2], summarization with FARMS [3] and improved probe set annotations [4] were used. Noisy genes were removed based upon their informative/non-informative (I/NI) calls [5].
[1] Verbist B, Klambauer G, Vervoort L, Talloen W, Shkedy Z, Thas O, Bender A, Gohlmann HW and Hochreiter S. Using transcriptomics to guide lead optimization in drug discovery projects: Lessons learned from the QSTAR project. Drug Discov Today. 2015; 20(5):505-513.
[2] Bolstad BM, Irizarry RA, Astrand M and Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003; 19(2):185-193.
[3] Hochreiter S, Clevert DA and Obermayer K. A new summarization method for Affymetrix probe level data. Bioinformatics. 2006; 22(8):943-949.
[4] Dai M, Wang P, Boyd AD, Kostov G, Athey B, Jones EG, Bunney WE, Myers RM, Speed TP, Akil H, Watson SJ and Meng F. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res. 2005; 33(20):e175.
[5] Talloen W, Clevert DA, Hochreiter S, Amaratunga D, Bijnens L, Kass S and Gohlmann HW. I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data. Bioinformatics. 2007; 23(21):2897-2902.

label: biotin

organism: Homo sapiens

source_name: melanoma

label_protocol: biotinylated cRNA was prepared using Ambion's MEGAScript T7 kit

growth_protocol: melanoma cells were grown as described in the manuscript

extract_protocol: QIAGEN's RNeasy Total RNA Isolation kit

treatment_protocol: cells were either grown in growth media or in growth media containing 1 mM 4-phenylbutyrate (4-PBA) for 48 hrs

tag: malignancy

value: metastatic


title: ex-vivo_culture_timepoint_4_patient_ID:_12298_2010-2012_Kilifi_Kenya 12298_T4

value: ex-vivo culture, timepoint 4, 12298, 2010-2012, Kilifi, Kenya, High, Expt B


title: MCM1DLN + PBA, sample 2 [experiment 1, biological replicate 2]


title: MCM1DLN, sample 4 [experiment 2, biological replicate 2]

description: metastatic melanoma cells, untreated

value: untreated


title: ex-vivo_culture_timepoint_5_patient_ID:_K0017_2008_Kisumu_Kenya K0017_T5

value: ex-vivo culture, timepoint 5, K0017, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_3_patient_ID:_J787/0_2010-2012_Kilifi_Kenya J787/0_T3

value: ex-vivo culture, timepoint 3, J787/0, 2010-2012, Kilifi, Kenya, High, Expt B


title: MCM1DLN, sample 3 [experiment 2, biological replicate 1]

description: metastatic melanoma cells, untreated


title: ex-vivo_culture_timepoint_4_patient_ID:_K0010_2008_Kisumu_Kenya K0010_T4

value: ex-vivo culture, timepoint 4, K0010, 2008, Kisumu, Kenya, High, Expt A

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_6_patient_ID:_K0007_2008_Kisumu_Kenya K0007_T6

value: ex-vivo culture, timepoint 6, K0007, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_10612b_2010-2012_Kilifi_Kenya 10612_T2

value: ex-vivo culture, timepoint 2, 10612b, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_K0008_2008_Kisumu_Kenya K0008_T7

value: ex-vivo culture, timepoint 7, K0008, 2008, Kisumu, Kenya, High, Expt A


title: MCM1DLN + PBA, sample 3 [experiment 2, biological replicate 1]


title: ex-vivo_culture_timepoint_5_patient_ID:_10581_2010-2012_Kilifi_Kenya 10581_T5

value: ex-vivo culture, timepoint 5, 10581, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_6_patient_ID:_10581_2010-2012_Kilifi_Kenya 10581_T6

source_name: P. falciparum (ex vivo), Kilifi, Kenya, TP6

value: ex-vivo culture, timepoint 6, 10581, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_10581_2010-2012_Kilifi_Kenya 10581_T3

value: ex-vivo culture, timepoint 3, 10581, 2010-2012, Kilifi, Kenya, High, Expt B


title: MCM1DLN + PBA, sample 4 [experiment 2, biological replicate 2]


title: MCM1G, sample 1 [experiment 1, biological replicate 1]

description: non-metastatic melanoma cells, untreated

value: non-metastatic


title: ex-vivo_culture_timepoint_5_patient_ID:_K0007_2008_Kisumu_Kenya K0007_T5

value: ex-vivo culture, timepoint 5, K0007, 2008, Kisumu, Kenya, High, Expt A


title: ex-vivo_culture_timepoint_2_patient_ID:_10581_2010-2012_Kilifi_Kenya 10581_T2

value: ex-vivo culture, timepoint 2, 10581, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_10555_2010-2012_Kilifi_Kenya 10555_T7

value: ex-vivo culture, timepoint 7, 10555, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_7_patient_ID:_10612b_2010-2012_Kilifi_Kenya 10612_T7

value: ex-vivo culture, timepoint 7, 10612b, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_3_patient_ID:_12182_2010-2012_Kilifi_Kenya 12182_T3

value: ex-vivo culture, timepoint 3, 12182, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_6_patient_ID:_10555_2010-2012_Kilifi_Kenya 10555_T6

value: ex-vivo culture, timepoint 6, 10555, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_12298_2010-2012_Kilifi_Kenya 12298_T1

value: ex-vivo culture, timepoint 1, 12298, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_5_patient_ID:_10612b_2010-2012_Kilifi_Kenya 10612_T5

value: ex-vivo culture, timepoint 5, 10612b, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_1_patient_ID:_12182_2010-2012_Kilifi_Kenya 12182_T1

value: ex-vivo culture, timepoint 1, 12182, 2010-2012, Kilifi, Kenya, High, Expt B


title: MCM1DLN, sample 2 [experiment 1, biological replicate 2]

description: metastatic melanoma cells, untreated

value: metastatic

value: untreated


title: MCM1G, sample 4 [experiment 2, biological replicate 2]


title: ex-vivo_culture_timepoint_4_patient_ID:_10612b_2010-2012_Kilifi_Kenya 10612_T4

value: ex-vivo culture, timepoint 4, 10612b, 2010-2012, Kilifi, Kenya, High, Expt B

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_6_patient_ID:_10612b_2010-2012_Kilifi_Kenya 10612_T6

value: ex-vivo culture, timepoint 6, 10612b, 2010-2012, Kilifi, Kenya, High, Expt B


title: MCM1DLN, sample 1 [experiment 1, biological replicate 1]

description: metastatic melanoma cells, untreated


title: ex-vivo_culture_timepoint_7_patient_ID:_10581_2010-2012_Kilifi_Kenya 10581_T7

value: ex-vivo culture, timepoint 7, 10581, 2010-2012, Kilifi, Kenya, High, Expt B


title: MCM1G, sample 3 [experiment 2, biological replicate 1]


title: ex-vivo_culture_timepoint_3_patient_ID:_10612b_2010-2012_Kilifi_Kenya 10612_T3

value: ex-vivo culture, timepoint 3, 10612b, 2010-2012, Kilifi, Kenya, High, Expt B


title: Zfpm1_21dpf_heart_rep3

type: SRA

city: Nanjing

first: Yuxi

last: Yang

state: Jiangsu

address: Room 402, 12 Xuefu Road, Nanjing University

department: Medical School

country: China

institute: Nanjing University

library_source: transcriptomic

data_processing:
Illumina bcl2fastq2-v 2.16.0.10 software was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Read quality was checked for each sample by using FastQC v 0.11.5.
High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters -q -p 8 --no-novel-juncs -G -o.
Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

organism: Danio rerio

source_name: heart

extract_protocol:
36hpf zebrafish embryos and 21dpf heart were collected respectively, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Magnetic beads with oligo(dT) were used to enrich the mRNAs, and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first-strand cDNA. Then double-stranded cDNA was synthesized by adding buffer solution, dNTPs and DNA polymeraseΙ. The double-stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions, then repaired at the tail ends, poly(A) added and enriched by PCR amplification. Finally, we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.

tag: strain

value: TU

value: heart

tag: developmental stage

tag: genotype

value: zfpm1 mutant


title: ex-vivo_culture_timepoint_2_patient_ID:_10555_2010-2012_Kilifi_Kenya 10555_T2

value: ex-vivo culture, timepoint 2, 10555, 2010-2012, Kilifi, Kenya, High, Expt B

source_name: P. falciparum lab-adapted strain P4, mix of samples collected across the 48-hour intraerythrocytic life cycle from synchronised in vitro cultures


title: ex-vivo_culture_timepoint_1_patient_ID:_10612b_2010-2012_Kilifi_Kenya 10612_T1

value: ex-vivo culture, timepoint 1, 10612b, 2010-2012, Kilifi, Kenya, High, Expt B


title: MCM1G, sample 2 [experiment 1, biological replicate 2]

value: non-metastatic


title: subject_2-BAT

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

country: USA

institute: Joslin Diabetes Center

hyb_protocol: 10ug of biotinylated cRNA were hybridized for 16hr at 45C to the array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Microarray data were normalized using robust multi-array average (RMA)

label_protocol: Biotin-labeled cRNA was synthesized, purified and fragmented using GeneChip 3’IVT Express Kit (Affymetrix).

growth_protocol: Immortalized progenitor cells were plated and grown in DMEM/H media (Dulbecco’s modified Eagle’s medium with 450mg/dl glucose) supplemented with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol: RNA was isolated using Direct-zol RNA MiniPrep kit (Zymo Research) according to the manufacturer’s instructions.

tag: subject id

value: subject 2

value: brown adipose tissue (BAT)

tag: cell type

value: preadipocytes


title: subject_2-WAT

value: white adipose tissue (WAT)


title: ex-vivo_culture_timepoint_1_patient_ID:_10581_2010-2012_Kilifi_Kenya 10581_T1

value: ex-vivo culture, timepoint 1, 10581, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_5_patient_ID:_10555_2010-2012_Kilifi_Kenya 10555_T5

value: ex-vivo culture, timepoint 5, 10555, 2010-2012, Kilifi, Kenya, High, Expt B


title: subject_3-WAT

value: subject 3


title: ex-vivo_culture_timepoint_2_patient_ID:_10555_2010-2012_Kilifi_Kenya 10555_T2dup

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_4_patient_ID:_10581_2010-2012_Kilifi_Kenya 10581_T4

value: ex-vivo culture, timepoint 4, 10581, 2010-2012, Kilifi, Kenya, High, Expt B


title: Zfpm1_21dpf_heart_rep1


title: ex-vivo_culture_timepoint_1_patient_ID:_10555_2010-2012_Kilifi_Kenya 10555_T1

value: ex-vivo culture, timepoint 1, 10555, 2010-2012, Kilifi, Kenya, High, Expt B


title: ex-vivo_culture_timepoint_4_patient_ID:_10555_2010-2012_Kilifi_Kenya 10555_T4

value: ex-vivo culture, timepoint 4, 10555, 2010-2012, Kilifi, Kenya, High, Expt B


title: 546N

status: Public on Dec 16 2017

city: Guangzhou

first: Zhaolei

last: Zeng

address: No. 651 Dong Feng Road East

department: Cancer Center

institute: Sun Yat-sen University

description: gene expression of CRC

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: colorecatal cancer adjacent tissue sample No.546

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

value: frozen tissue

value: Male

tag: age


title: 587N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.587


title: 615N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.615

value: Female


title: Ctrl_21dpf_heart_rep3

value: TU

value: heart

value: control


title: 419N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.419


title: subject_3-BAT


title: Ctrl_21dpf_heart_rep1


title: Zfpm1_21dpf_heart_rep2

value: zfpm1 mutant


title: 527N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.527


title: Ctrl_21dpf_heart_rep2


title: 389N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.389


title: 372N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.372


title: ex-vivo_culture_timepoint_3_patient_ID:_10555_2010-2012_Kilifi_Kenya 10555_T3

value: ex-vivo culture, timepoint 3, 10555, 2010-2012, Kilifi, Kenya, High, Expt B


title: 86N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.86


title: subject_1-BAT

value: subject 1

value: brown adipose tissue (BAT)

value: preadipocytes


title: 584N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.584


title: 615T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.615


title: 1187N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.1187


title: 538N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.538


title: 573N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.573


title: subject_1-WAT

value: white adipose tissue (WAT)


title: 711T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.711


title: 538T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.538


title: 397T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.397


title: 503N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.503


title: 711N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.711


title: 503T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.503


title: 389T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.389


title: 440N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.440


title: 1187T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.1187


title: 404N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.404


title: 93N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.93


title: 352N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.352


title: 397N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.397


title: 584T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.584


title: 404T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.404


title: 12N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.12


title: 419T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.419


title: 527T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.527


title: 283N

description: gene expression of CRC

source_name: colorecatal cancer adjacent tissue sample No.283


title: 440T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.440


title: 573T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.573


title: 546T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.546


title: 372T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.372


title: HBEC4_vector

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description: cells with empty retroviral vector

hyb_protocol: As recommended by manufacturer

scan_protocol: GeneChip Scanner 3000 7G was used for scanning.  Affymetrix GeneChip Operating software (GCOS v1.4) was used for image processing

data_processing: Data was normalized by justRMA function in affy package (R/Bioconductor).

source_name: HBEC4, empty retroviral vector

label_protocol: As recommended by manufacturer

growth_protocol: Grown in Keratinocyte medium supplemented with 30ug/ml Bovine Pituitary Extract (BPE) and 0.2ng/ml recombinant Epidermal Growth Factor (EGF), all from Invitrogen (#17005-042).

extract_protocol: Total RNA was extracted using Qiagen's Rneasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Transduced cells underwent two weeks of antibiotic selection (100ug/ml hygromycin). They were then passaged three times in plain growth medium and harvested upon reaching 75% confluency.

value: Human bronchial epithelial cells immortalized with hTERT and hCDK4

tag: patient age

tag: patient gender

tag: patient smoking status

value: Smoker

tag: patient diagnosis

value: With lung cancer as cells isolated from large airway

tag: snail oe

value: no


title: 86T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.86


title: kynurenic acid treated, technical rep3

city: Stockholm

first: Leandro

middle: Z.

last: Agudelo

state: Stockholm

address: von eulers väg 8, plan 3

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from kynurenic acid treated inguinal fat cells

hyb_protocol: 2.5ug of ss DNA target was hybridized for 18h at 48C° to a Mouse Gene 2.1 ST Array Plate, washed and stained in the Gene Titan Instrument 400.

scan_protocol: not provided

data_processing: The data was RMA processed in Expression Console (V.1.41). Data was log2 transformed. Statistical analysis for comparisons of different treatment groups: Student's t-test, unpaired, 2-sided.

source_name: inguinal primary adypocytes  treated for 12h with Kynurenic acid

label_protocol: 100ng of total RNA was used to generate amplified sense strand DNA targets with Affymetrix WT Plus Reagent Kit followed by fragmentation and biotinylation with Affymetrix WT Terminal Labeling Kit.

extract_protocol: RNA was extracted by Isol reagent according to manufacturer's protocol

value: white adipose tissue


title: kynurenic acid treated, technical rep2


title: PBS treated, technical rep2

description: Gene expression data from PBS treated inguinal fat cells

source_name: inguinal primary adypocytes  treated for 12h with PBS


title: kynurenic acid treated, technical rep1


title: 587T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.587

value: frozen tissue


title: 93T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.93


title: PBS treated, technical rep3


title: 12T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.12

value: Male


title: WS8_Veh_B2

city: Durham

first: Jeff

last: Jasper

state: NC

department: Pharmacology and Cancer Biology

institute: Duke University

description:
MCF7-derived 4-OHT sensitive
Processed data file: All_Samples_noTSS_raw_counts.txt

library_source: genomic

data_processing:
Aligned using BWA.
Peak calling using F-Seq.
DESeq for differential peaks.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: All_Samples_noTSS_raw_counts.txt: Raw counts for each sample across the union of candidate DNase sites.
Supplementary_files_format_and_content: DESEQ_WS8-Veh_vs_TAMR-Veh_peaks_dn.bed: File with columns: chr, start, stop, name, log2FC, FDR.
Supplementary_files_format_and_content: DESEQ_WS8-Veh_vs_TAMR-Veh_peaks_up.bed: File with columns: chr, start, stop, name, log2FC, FDR.
Supplementary_files_format_and_content: (sample)_dnase_peaks.bed: Peaks identified by F-Seq. Format: chr, start, stop, score.
Supplementary_files_format_and_content: bigWig files were generated from F-Seq outputs using WigtobigWig.

molecule: genomic DNA

growth_protocol: Cells were plated in CFS in 15cm plates for 48 hours before treatment.

extract_protocol: DNase-Seq was performed as previously described (Song and Crawford 2010; Song, Zhang et al. 2011).

treatment_protocol: Treated with either vehicle or 4-OHT for 24 hours.

tag: cell line

value: VEH

tag: replicate


title: HBEC4_SnailOE

description: cells with SNAI1 overexpression

source_name: HBEC4, retroviral vector with SNAI1 cDNA

value: Female

value: yes


title: 283T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.283

tag: tissue


title: PBS treated, technical rep1


title: TAMR_Veh_B2

description:
MCF7-derived 4-OHT resistant
Processed data file: All_Samples_noTSS_raw_counts.txt

source_name: TAMR

value: TAMR


title: HBEC3_vector

description: cells with empty retroviral vector

source_name: HBEC3, empty retroviral vector

value: No lung cancer as cells isolated from large airway


title: TAMR_Tam_B1


title: 352T

description: gene expression of CRC

source_name: colorecatal cancer tissue sample No.352

tag: gender


title: TAMR_Veh_B1

tag: treatment


title: MCF7_Veh_B1

description:
MCF7
Processed data file: All_Samples_noTSS_raw_counts.txt


title: MCF7_Tam_B2


title: WS8_Tam_B1


title: WS8_Tam_B2


title: WS8_Veh_B1


title: Sperm 19

type: genomic

city: Salt Lake City

first: Douglas

last: Carrell

state: UT

address: 675 Arapeen Dr. Suite 201

institute: University of Utah

description: Donor human sperm

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

source_name: Donor human sperm

label_protocol: Standard Illumina Protocol

extract_protocol: DNEasy kit to extract sperm DNA followed by Zymo EZ bisulfite conversion kit

tag: tag

value: Sperm


title: HBEC3_SnailOE

description: cells with SNAI1 overexpression

source_name: HBEC3, retroviral vector with SNAI1 cDNA


title: MCF7_Veh_B2


title: TAMR_Tam_B2


title: Sperm 20

description: Donor human sperm


title: Sperm 11

description: Donor human sperm


title: MCF7_Tam_B1


title: Sperm 14

description: Donor human sperm


title: Sperm 12

description: Donor human sperm


title: Sperm 6

description: Donor human sperm


title: Sperm 5

description: Donor human sperm


title: Sperm 18

description: Donor human sperm


title: Sperm 17

description: Donor human sperm


title: T8.MP.LCMV.d7.Sp.rep1

status: Public on Dec 15 2017

city: La Jolla

first: John

middle: Justin

last: Milner

state: CA

address: 9500 Gilman Dr. MC0377

institute: UCSD

data_processing:
Reads were aligned to mm10 by bowtie.
Only unique reads were kept.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bedgraph

source_name: D7 Spleen KLRG1lo CD127hi

extract_protocol:
Single cell suspensions from the spleen were sorted by FACS.
The ATAC-Seq library was generated by Nextera sample prep kit (Illumina).

treatment_protocol: Day 7 LCMV infection.

tag: strain

value: 6-14 weeks

value: Spleen

value: KLRG1lo CD127hi CD8+ T cell


title: Sperm 16

description: Donor human sperm


title: T8.MP.LCMV.d7.Sp.rep2


title: Clean 4

description: Free of somatic cells

source_name: Free of somatic cells


title: Sperm 15

description: Donor human sperm


title: Clean 3

description: Free of somatic cells


title: Contaminated 5

description: Somatic cell contamination

source_name: Somatic cell contamination


title: GBM derived Sphere line_LN-2669GS

city: Lausanne

first: Pierre

last: Bady

address: Quartier UNIL-Sorge

department: Swiss Institute of Bioinformatics

country: Switzerland

institute: CHUV / BCF / SIB

description: GBM derived sphere line

hyb_protocol: Following probe denaturation and pre-annealing with Cot-1 DNA, hybridization was performed at 65°C with rotation for 40 hr. Four steps were done with Agilent Oligo CGH washes: Wash buffer 1 at room temperature for 5 min, wash buffer 2 at 37°C for 1 min, an acetonitrile rinse at room temperature for 1 min and a 30 sec wash at room temperature in Agilent's Stabilization and Drying Solution

scan_protocol: Arrays were scanned using an Agilent DNA Microarray Scanner

data_processing: Data was extracted using Agilent Feature Extraction Software v.9.5.3.1 using default CGH extraction parameters

source_name: GBM derived Sphere line_LN-2669GS

label_protocol: The test and reference DNAs are digested with Alu I and Rsa I (Promega, Madison, WI), and purified with the QIAprep Spin Miniprep kit (QIAGEN, Germantown, MD). Test DNA (1 µg) and reference DNA (1 µg; Promega) were labeled by random priming with either Cy3-dUTP or Cy5-dUTP using the Agilent Genomic DNA Labeling Kit Plus. Following the labeling reaction the individually labeled test and reference samples were concentrated using Microcon YM-30 filters (Millipore, Billerica, MA) and then combined.

extract_protocol: DNA was extracted ffollowing standard protocols (Agilent Human Genome CGH Microarray Kit 44A).

tag: disease

value: GBM

source_name: reference

tag: sample type

value: Promega reference


title: Sperm 4

description: Donor human sperm


title: Sperm 2

description: Donor human sperm


title: GBM

description: GBM

source_name: GBM


title: Sperm 7

description: Donor human sperm


title: Sperm 9

description: Donor human sperm


title: adherent GBM derived cell line_LN-2669

description: adherent GBM cell line

source_name: adherent GBM derived cell line_LN-2669


title: adherent GBM derived cell line_LN-2207

description: adherent GBM cell line

source_name: adherent GBM derived cell line_LN-2207


title: Sperm 3

description: Donor human sperm


title: GBM derived Sphere line_LN-2288GS

description: GBM derived sphere line

source_name: GBM derived Sphere line_LN-2288GS


title: T8.TE.LCMV.d7.Sp.rep1

source_name: D7 Spleen KLRG1hi CD127lo

value: KLRG1hi CD127lo CD8+ T cell


title: GBM derived Sphere line_LN-2683GS, recurrent from GBM TuBa2758

description: GBM derived sphere line


title: GBM derived Sphere line_LN-2540GS

description: GBM derived sphere line

source_name: GBM derived Sphere line_LN-2540GS


title: T8.TE.LCMV.d7.Sp.rep2


title: Clean 1

description: Free of somatic cells


title: Sperm 13

description: Donor human sperm


title: Clean 2

description: Free of somatic cells


title: Contaminated 1

description: Somatic cell contamination


title: D23580_pool_TEX

city: Liverpool

first: Jay

last: Hinton

address: Crown Street

department: Institute of Integrative Biology

country: United Kingdom

institute: University of Liverpool

data_processing:
Reads were de-multiplexed and sequence reads were then mapped on the S. Typhimurium 4/74 reference genome using Segemehl with accuracy set to 100%.
To increase mapping quality, unmapped reads were sequentially truncated by one nucleotide from the end of the read and were mapped again. This process was iterated until a minimal read length of 20 nucleotides or until a read mapped into a single location on the chromosome.
Read pileups for each sample were normalised to the smallest library and converted to .sgr files to visualise mapped reads in the Integrated Genome Browser (IGB).
Genome_build: FN424405
Supplementary_files_format_and_content: .sgr files are provided showing uniquely mapped sequence reads (normalization). Ready to load into Integrated Genome Browser (IGB). The file consists of two columns showing nucleotide position on the chromosome and number of reads mapped at each location. "Plus" and "Minus" refer to the strands of the Salmonella chromosome.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

source_name: Salmonella enterica, pool, TEX

growth_protocol: All environmental growth conditions were repeated exactly as previously described (Kroger et al., 2013 Cell host microbe) with the exception that the ‘pool’ sample was obtained by pooling RNA from 16 environmental conditions (EEP, MEP, LEP, ESP, LSP, 25°C, NaCl shock, Bile shock, Low Fe2+ shock, Anaerobic shock, Anaerobic growth, Oxygen shock, NonSPI2, InSPI2, Peroxide shock (InSPI2) and Nitric oxide shock (InSPI2)).

extract_protocol:
Total RNA was extracted using Trizol, and treated with DNase I as described previously (Kroger et al., 2012 PNAS). RNA integrity was inspected visually with the Bioanalyzer (Agilent Technologies). Contaminating DNA was removed using DNase I (Ambion) and RNA samples were not ribo-depleted prior to cDNA library construction.
cDNA library construction, TEX-treatment for dRNA-seq (ESP, InSPI2 and pooled sample) and RNA-seq with the Illumina HiSeq platform was carried out by Vertis Biotechnologie, Germany. All protocols were identical to those used previously (Kroger et al., 2012; Kroger et al., 2013).

tag: growth condition

value: Pooled RNA from all conditions

tag: tex treatment


title: Sperm 10

description: Donor human sperm


title: D23580_ESP_TEX

source_name: Salmonella enterica, ESP, TEX

value: Early stationary phase


title: Contaminated 2

description: Somatic cell contamination


title: Sperm 1

description: Donor human sperm


title: Human epidermal tissue, SMRT-2 siRNA, rep 1

city: Stanford

first: Aparna

last: Bhaduri

address: 269 Campus Drive

institute: Stanford University

hyb_protocol: Hybridization to the Affymetrix Gene Chip HG-U133 Plus 2.0 arrays was carried out at Stanford’s PAN facility.

scan_protocol: Not provided

data_processing: affy bioconductor R package using the justRMA command

source_name: SMRT-2 depleted human epidermal tissue

label_protocol: Labeling of cDNA derived from control and SMRT-2-deficient human progenitor keratinocytes was done using the MessageAmp III RNA amplification kit (Ambion) following the manufacturer’s instructions.

growth_protocol: Primary human epidermal keratinocytes were isolated from fresh surgical specimens. Devitalized human acellular dermis was used as the supporting framework for organotypic cultures. Transduced keratinocytes were seeded onto the basement membrane side of dermis, and tissues were maintained in dual chamber supports without fibroblasts. For SMRT-2 knockdown, RNA interference was performed using 1 nmol of siRNA per 1 million cells using nucleofection (Lonza) according to the manufacturer’s recommendations for keratinocytes.

extract_protocol: RNA was isolated from regenerated human epidermal tissue using RNeasy Plus Mini Kit (Qiagen)

tag: age

value: 3 days post-seeding onto dermis

value: Regenerated human epidermal tissue

tag: genotype

value: SMRT-2 knockdown


title: Human epidermal tissue, control siRNA, rep 2

source_name: wild type human epidermal tissue

value: Wild type


title: D23580_ESP

source_name: Salmonella enterica, ESP

value: no


title: Human epidermal tissue, SMRT-2 siRNA, rep 2


title: D23580_pool

source_name: Salmonella enterica, pool


title: BCG-iv [scRNA-seq]

city: Chicago

first: Luis

last: Barreiro

state: Illinois

address: 900 E 57th Street

institute: University of Chicago

data_processing:
bcl2fastq was used to get the demultiplexed datasets from the sequencing machine.
Sample preprocessing was done using the count command of CellRanger (Zheng et al., 2017) against the mm10 1.2.0 reference genome. As part of the different QC filters, we filtered out cells (i) expressing less than 500 genes, (ii) with an high fraction of mitochondrial RNA reads (������!"#$>4.7%), (iii) with a low number of UMIs (������!"#<2400������!"#), or (iv) with a low percentage of protein-coding genes (������!"<92.5������!") (these thresholds were set upon visual inspection; Figure S4A). After these QC steps we kept a total of 7,666 cells (5,872 and 1,794 cells in PBS and BCG, respectively). In addition to removing lower quality cells, we limited all downstream analyses to genes that were expressed in at least 5 cells, corresponding to 14,751 genes.
We used the function computeSumFactors, from the R package scran (Lun et al., 2016) to normalize the data. This method works by declaring a series of cell pools whose expressions are added and normalized against a common reference. Each of these pools is then interpreted as a linear system from which the contribution of each single cell can be deconvolved, allowing the inference of cell-wise normalization factors in a way that is robust against noise and low expression levels. To ensure that a majority of genes are not DE between any of the pools and the common reference that they are normalized against, clusters of homogeneous gene expression are first built using the function quickCluster. Thus, cell specific normalization factors are inferred within each cluster, and then rescaled by normalization between clusters.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger output files (tsv, mtx, h5)

source_name: LKS+ Hematopoietic stem cells

extract_protocol: Single-cell GEMs were generated using a Chromium Controller instrument (10x Genomics). Sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kits (10x Genomics), according to the manufacturer’s instructions. Briefly, GEM-RT was performed in a thermal cycler: 53°C for 45 min, 85°C for 5 min. cDNA was cleaned up with DynaBeads MyOne Silane Beads (ThermoFisher Scientific) and amplified with a thermal cycler: 98°C for 3 min, cycled 12 x 98°C for 15 s, 67°C for 20s, 72°C for 1 min, and 72°C 1 min. After a cleanup with SPRIselect Reagent Kit, the libraries were constructed by performing the following steps: fragmentation, end-repair, A-tailing, SPRIselect cleanup, adaptor ligation, SPRIselect cleanup, sample index PCR, and SPRIselect size selection. Libraries were sequenced on an Illumina HiSeq 4000 with 100 bp paired-end reads.

tag: cell type

value: LKS+ Hematopoietic stem cells

value: BCG iv


title: Contaminated 3

description: Somatic cell contamination


title: PBS [scRNA-seq]

value: PBS iv


title: D23580_inSPI2_TEX

source_name: Salmonella enterica, inSPI2, TEX

value: SPI-2 inducing

value: yes


title: Clean 5

description: Free of somatic cells

source_name: Free of somatic cells

value: Sperm


title: Contaminated 4

description: Somatic cell contamination

source_name: Somatic cell contamination


title: GBM derived Sphere line_LN-2207GS

description: GBM derived sphere line

source_name: GBM derived Sphere line_LN-2207GS

source_name: reference


title: Sperm 8

description: Donor human sperm

source_name: Donor human sperm


title: Human epidermal tissue, control siRNA, rep 1


title: D23580_inSPI2

source_name: Salmonella enterica, inSPI2


title: Kid_D35#2

description: Gene expression data from various CD8+ T cell subsets

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: Data was processed in GenePattern.

label: Biotin

source_name: D35 Kidney P14

label_protocol: Affy GeneChip WT cDNA synthesis kit/cRNA cleanup kit

extract_protocol: RNA was extracted using Trizol per manufacturer's instruction.

treatment_protocol: Naïve P14s were transferred into recipent mice and then infected with LCMV. P14 CD8+ T cell subsets were sorted on D7 or D35 of infection.

value: Kidney

tag: time point

value: day 35


title: Tcm_D35#2

source_name: D35 Spleen CD62L+ P14

value: Spleen


title: OS195_oxygen_2

city: Norman

first: Jie

last: Deng

state: OK

address: 101 David L Boren Blvd, SRTC 2022

institute: University of  Oklahoma

description:
X195DO; OS195DO
The same reference sample was labeled Cy3 on all arrays

hyb_protocol: For each hybridization, 10 μl of labeled cDNA from OS185 or OS195 was mixed with an equal volume of labeled reference cDNA. Hybridization reaction was at 50 °C for 18 h.

scan_protocol: Arrays were and scanned using an Axon GenePix 4000B scanner. For each array, Cy3 and Cy5 signals were normalized to the arithmetic mean of ratios using the GenePix software.

data_processing: Features having fewer than 50% of pixels with signal more than two standard deviations above background in both channels were excluded in downstream analysis. Genes showing significantly different expression levels between pair-wise comparisons among the three growth conditions were identified using Significance Analysis of Microarrays (Tusher et al., 2001).

organism: Shewanella baltica

label_protocol: Resuspend pellets in 4.5uL 100 mM Na2CO3.  Mix with 4.5 uL Cy5 or Cy3, Incubate at 25C for 1.5 hrs, Clean-up with Qiagen Min-Elute PCR purification kit

growth_protocol: Cells were grown aerobically in HEPES medium or anaerobically with supplementation of 5 mM sodium nitrate or 10 mM sodium at 22 °C.

extract_protocol: RNA was extracted from cell pellets using a Qiagen RNeasy kit, followed by reverse transcription with random primers at 25 °C for 10 min, 42 °C for 70 min, and 70 °C for 15 min (Invitrogen). Labeled cDNAs were purified with QiaQuick MinElute PCR purification columns and eluted in 12 μl of RNase‐free water (Qiagen).

treatment_protocol: Aerobic growth, or anerobic nitrate or thiosulfate respiring growth condition

value: aerobic condition

source_name: Total RNA from cells of four strains OS155, OS185, OS195 and OS223 grown under conditions of respiring fumarate, nitrate, thiosulfate and under aerobic condition.


title: IEL_D35#2

source_name: D35 IEL P14

value: Small Intestine Epithelium


title: IEL_D35#1


title: Sp_D7#2

source_name: D7 Spleen P14

value: day 7


title: Sp_D7#3


title: Tem_D35#1

source_name: D35 Spleem CD62l- P14


title: OS195_oxygen_1

description:
X195CO; OS195CO
The same reference sample was labeled Cy3 on all arrays


title: PBL_D7#3

source_name: D7 PBL P14

value: PBL


title: Tem_D35#2


title: Kid_D35#1


title: Tcm_D35#1


title: OS195_nitrate_1

description:
X195CN; OS195CN
The same reference sample was labeled Cy3 on all arrays

value: anaerobic  nitrate respiratory condition