title: WT lung CD103 #3

description: tissue dissection, FACS Aria sorted

source_name: WT lung CD103 #3

value: BRAFV600E(CA-flox) / CD11c-Cre(neg)

value: WT BRAF


title: WT lung CD103 #1

status: Public on Dec 20 2017

type: RNA

city: New York

first: Brandon

last: Hogstad

state: NY

address: 1470 Madison Ave

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: tissue dissection, FACS Aria sorted

hyb_protocol: Expression Analysis, Inc standard protocol using Hybridization, Wash and Stain kit (Affymetrix)

scan_protocol: Expression Analysis, Inc standard protocol using Affymetrix GeneChip Scanner

data_processing:
Immgen.org data QC protocol: http://www.immgen.org/Protocols/ImmGen%20QC%20Documentation_ALL-DataGeneration_0612.pdf
Expression normalized across the entire group according to Immgen data QC protocol: http://www.immgen.org/Protocols/ImmGen%20QC%20Documentation_ALL-DataGeneration_0612.pdf

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: WT lung CD103 #1

label_protocol: Expression Analysis, Inc standard biotin labeling protocol.

growth_protocol: Control and CD11c-Cre/BRAFV600E(flox) mice were aged to 14 weeks old before harvesting organs. BMDCs were derived from bone marrow obtained from femur bones of 5 week old control and CD11c-Cre/BRAFV600E(flox) mice.

extract_protocol: Immgen.org standard protocol for total RNA extraction with Trizol

treatment_protocol: Control and CD11c-Cre/BRAFV600E(flox) mice were unmanipulated before organ harvest. BMDCs cultures were untreated before harvest.

tag: genotype

tag: braf status

tag: organ of origin

value: Lung

tag: cell type


title: BRAF BMDC #1

description: FACS Aria sorted (live CD11c+CD11b+ BMDC)

source_name: BRAF BMDC #1

value: bone marrow

value: BMDC


title: NS-GFP4+_LSK3

city: Kanazawa

first: Atsushi

last: Hirao

address: kakuma

department: Division of Molecular Genetics

country: Japan

institute: kanazawa university

hyb_protocol: Not provided

scan_protocol: Not provided

data_processing: Expression data was processed with GeneSpring 12.6GX, using quantile normalization with no baseline transformation.

source_name: sorted murine LSK cells from bone marrow

label_protocol: Samples were processed by Hokkaido System Science Co.,Ltd.(Japan), and run on Agilent SurePrint G4 mouse gene expression arrays (single color).

extract_protocol: Total RNA from 1x 10E4 each fractionated LSK cells based on NS-GFP level  was isolated by using TRIzol (Invitrogen).

tag: strain background

tag: tissue

value: sorted NS-GFP4+ LSK cells


title: WT lung CD11b #3

description: tissue dissection, FACS Aria sorted

source_name: WT lung CD11b #3


title: WT lung CD11b #1

description: tissue dissection, FACS Aria sorted

source_name: WT lung CD11b #1


title: 6 wk DMM-2

city: Melbourne

first: John

last: Bateman

address: Flemington Road

department: Skeletal Biology

country: Australia

institute: Murdoch Childrens Research Institute

description: Bilateral surgeries performed. Knees taken from the same mouse for both histology and expression profiling.

hyb_protocol: miRNA expression profiling was performed at the Ramaciotti Centre for Genomics (UNSW, Sydney, Australia). miRNA expression profiling was performed using SurePrint mouse miRNA microarray technology, release 21 (G4859C, Agilent Technologies). Briefly, 100ng of total RNA was labelled and hybridized using the miRNA microarray System with miRNA complete labelling and Hyb kit version 3.0 (Agilent Technologies) by following manufacturer’s instructions. Randomized placement of samples on the arrays was performed.

scan_protocol: The arrays were scanned on a G2565CA microarray scanner and the features were extracted using Agilent Feature Extraction 12.0.07 software

data_processing: The raw microarray data was processed in statistical language R, using the limma package (limma_3.20.9) and background corrected with Normexp, normalized within arrays with cyclic loess. Only probes with 10% greater signal than the negative controls in at least 5 samples were maintained for differential expression analysis. Probes were summarised at the gene level and the data was adjusted for multiple testing using Benjamini-Hochberg method to control for false discovery rate.

label: Cyanine 3-pCp

source_name: Synovium (Anterior)

growth_protocol: Mice with DMM and sham surgery were co-housed 2-5 animals/30×20×18cm individually-ventilated-cage with filter lids, provided with sterilised bedding and environmental enrichment, maintained at 21-22°C with a 12-hour light/dark cycle, and received water and complete pelleted food ad libitum. Mice received no post-arthritis-induction medication and were allowed unrestricted cage exercise. Animals were sacrificed at 1 and 6 weeks after surgery.

extract_protocol: The anterior synovial tissues (comprising the joint capsule plus synovial lining plus infrapatellar fat pad, excluding muscle) were isolated using a dissecting microscope.

treatment_protocol: Sixteen animals had bilateral DMM surgery. Briefly, under isoflurane anaesthesia, the medial menisco-tibial ligament was exposed by medial para-patellar arthrotomy and intrapatellar fat pad elevation, and transected with curved dissecting forceps by one surgeon (CBL). Joints were flushed with sterile saline prior to separate closure of the joint capsule, subcutaneous tissue (8/0 polyglactin 910 suture) and skin (cyanoacrylate). Bilateral sham-operations were performed in 16 age- and sex-matched mice, where all procedures were identical except the medial menisco-tibial ligament was visualised but not transected. Mice were randomly allocated to DMM/sham and harvest time

tag: strain

tag: gender

value: Male

tag: stress

value: DMM

tag: post surgery time point

value: 6 wk


title: 1 wk sham-2

label_protocol: miRNA expression profiling was performed at the Ramaciotti Centre for Genomics (UNSW, Sydney, Australia). miRNA expression profiling was performed using SurePrint mouse miRNA microarray technology, release 21 (G4859C, Agilent Technologies). Briefly, 100ng of total RNA was labelled and hybridized using the miRNA microarray System with miRNA complete labelling and Hyb kit version 3.0 (Agilent Technologies) by following manufacturer’s instructions. Randomized placement of samples on the arrays was performed.

value: sham

value: 1 wk


title: 6 wk sham-3


title: 6 wk DMM-4


title: 1 wk DMM-4


title: 6 wk DMM-3


title: 1 wk DMM-2


title: WT BMDC #2

source_name: WT BMDC #2


title: NS-GFP2+_LSK2

value: sorted NS-GFP2+ LSK cells


title: 1 wk DMM-3


title: 1 wk sham-4


title: 6 wk sham-4


title: 1 wk sham-3


title: WT liver CD11b #3

description: tissue dissection, FACS Aria sorted

source_name: WT liver CD11b #3

value: Liver


title: WT BMDC #3

source_name: WT BMDC #3


title: AGS cells infected with H. Pylori at 100 MOI_1_miRNA

city: Kolkata

first: Manikuntala

last: Kundu

state: West Bengal

address: 93/1, Acharya Prafulla Chandra Road

country: India

institute: Bose Institute

description: miRNA expression of infected AGS cells

hyb_protocol: Agilent miRNA Hybridization kit (Cat # 5190-0411) was used

scan_protocol: Scanned Using Agilent Scanner

data_processing:
Percentile Shift Normalization to the 75th percentile
Log2 transformed signal intensity values; Percentile Shift normalization to the 75th percentile

organism: Homo sapiens

source_name: AGS cells infected with H. Pylori at 100 MOI, miRNA, replicate 1

label_protocol: Agilent miRNA labeling reagent and Hybridization Kit (Cat # 5190-0431) was used. The method involves ligation of one Cy3 –pCp molecule to the 3’ end of RNA molecule with greater than 90% efficiency that generates fluorescent miRNA.

growth_protocol: The human gastric epithelial cell line AGS was obtained from the National Centre of Cell Science (Pune, India) and maintained in Ham’s F-12 (Invitrogen) medium supplemented with 10% heat-inactivated FBS, 100U/ml penicillin and 100µg/ml streptomycin at 37oC in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted from 106 AGS cells using the mirVana miRNA isolation kit (Ambion) according to the manufacturer’s instructions.

treatment_protocol: AGS cells were infected with H. pylori 26695 at 100 MOI for 4 h,  washed and RNA was isolated from the cells. Uninfected cells were also maintained for the same time point, following which cells were harvested for RNA isolation.

tag: cell line

value: Gastric epithelial cell line, AGS

tag: infected with

value: H. pylori 26695 at 100 MOI, for 4 hrs


title: 6 wk sham-1


title: Uninfected AGS cells_2_miRNA

description: miRNA expression of uninfected AGS cells

source_name: Uninfected AGS cells, miRNA, replicate 2

value: Uninfected


title: WT BMDC #1

source_name: WT BMDC #1


title: WT liver CD11b #1

description: tissue dissection, FACS Aria sorted

source_name: WT liver CD11b #1


title: AGS cells infected with H. Pylori at 100 MOI_2_miRNA

description: miRNA expression of infected AGS cells

source_name: AGS cells infected with H. Pylori at 100 MOI, miRNA, replicate 2


title: Uninfected AGS cells_1_miRNA

source_name: Uninfected AGS cells, miRNA, replicate 1


title: 6 wk DMM-1


title: 6 wk sham-2


title: 1 wk sham-1


title: 1 wk DMM-1


title: 1 wk DMM-1

hyb_protocol: mRNA expression profiling was performed using SurePrint mouse mRNA expression V2 microarray technology (G4852B, Agilent Technologies). Briefly, 100ng of total RNA was labelled and hybridized using the low input quick amp WT labelling kit (Agilent Technologies) by following manufacturer’s instructions. Randomized placement of samples on the arrays was performed.

data_processing: The raw microarray data was processed in statistical language R, using the limma package (limma_3.20.9) and background corrected with Normexp, normalized within arrays with cyclic loess. This synovial mRNA array data was normalised with mRNA array data from subchondral bone tissue from the same cohort of mice as part of a separate study (GSE101573). Only probes with 10% greater signal than the negative controls in at least 5 samples were maintained for differential expression analysis. Probes were summarised at the gene level and the data was adjusted for multiple testing using Benjamini-Hochberg method to control for false discovery rate.


title: MESA_smoker_G9

status: Public on Dec 19 2017

type: SRA

city: Research Triangle Park

first: Douglas

middle: A.

last: Bell

state: NC

address: PO Box 12233

department: Immunity Inflammation and Disease Lab

institute: National Institute of Environmental Health Sciences

library_source: genomic

data_processing:
Aligned with Bismark version 0.14.3 with the following parameters: -I 0 -X 1000
Average methylation percentages of all the individual samples within a specified group are available on the series record.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_coverage_bedGraph: read coverage in bedGraph format.
Supplementary_files_format_and_content: *_methpct_bedGraph: CpG methylation percentages in bedGraph format.

molecule: genomic DNA

source_name: human CD14+ cells from adult peripheral blood

extract_protocol:
CD14+ cells were isolated using anti-CD14+ antibody-coated magnetic beads (Invitrogen) from MNCs of adult peripheral blood.
RRBS libraries were generated from 100-300ng genomic DNA of circulating CD14+ monocytes for each subject, and sequenced as previously described (Boyle et al. 2012). Briefly, genomic DNA was cut with Msp I followed by end repairing, “A” tailing, barcoded adapter ligation, bisulfite conversion, and PCR amplification for RRBS library generation.
Illumina RNA TruSeq Kit, QIAGEN EpiTect Bisulfite and MinElute Gel Extraction Kits.

treatment_protocol: DNA samples were treated with bisulfite conversion using QIAGEN EpiTect Bisulfite and MinElute Gel Extraction Kits.

value: primary circulating CD14+ cells

tag: smoking status

value: smoker

tag: population

value: MESA


title: MESA_smoker_H3


title: 6 wk sham-4

label_protocol: mRNA expression profiling was performed using SurePrint mouse mRNA expression V2 microarray technology (G4852B, Agilent Technologies). Briefly, 100ng of total RNA was labelled and hybridized using the low input quick amp WT labelling kit (Agilent Technologies) by following manufacturer’s instructions. Randomized placement of samples on the arrays was performed.


title: MESA_smoker_H1


title: MESA_smoker_G7


title: MESA_smoker_H7


title: MESA_smoker_H5


title: 6 wk DMM-1


title: 6 wk DMM-3


title: 1 wk sham-2


title: 1 wk DMM-2


title: 1 wk DMM-4


title: 6 wk sham-2


title: 6 wk DMM-4


title: 1 wk sham-3


title: 1 wk sham-4


title: 6 wk sham-3


title: 1 wk DMM-3


title: 1 wk sham-1


title: 6 wk DMM-2


title: 6 wk sham-1


title: MESA_smoker_G5


title: MESA_smoker_G3


title: MESA_smoker_G1


title: MESA_smoker_F1


title: MESA_smoker_F3


title: MESA_smoker_F9


title: MESA_smoker_F5


title: MESA_smoker_E7


title: MESA_smoker_D7


title: MESA_smoker_C5


title: MESA_smoker_C7


title: MESA_smoker_C9


title: MESA_smoker_E5


title: MESA_smoker_C1


title: MESA_smoker_D3


title: MESA_smoker_E9


title: MESA_smoker_D9


title: BT549 miR-200c A

city: Aurora

first: Jessica

last: Christenson

state: CO

department: Pathology

institute: University of Colorado Anschutz Medical Campus

hyb_protocol: One ug of biotinylated RNA from each sample was hybridized onto AffymetrixÂ® Human Gene 1.0 ST array according to the manufacturer's recommendations.

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

data_processing: Affymetrix CEL files from all samples hybridized to the mRNA arrays were loaded on to Partek Genoimcs Suite. Signal intensities for all probe sets were obtained using Robust Multichip Averaging summarization algorithm which involves three steps - background correction, quantile normalization and probe summarization (median polish). Quality control was performed by principal component analysis to identify outliers (no outliers detected).

source_name: Human TNBC cell line

label_protocol: One ug of total RNA from each sample was labelled with FlashTag Biotin RNA Labeling kit (Genisphere, Hatfield, PA, USA).

growth_protocol: Cells grown in attached culture conditions in RPMI + 10% FBS

extract_protocol: RNA extracted using the Qiagen RNeasy Plus kit, following the manufacturer's instructions.

treatment_protocol: Cells were grown in RPMI + 10% FBS ± 1ug/mL doxycycline, 48 hours.

value: TNBC

tag: treatment

value: 1ug/mL doxycycline, 48 hours


title: MESA_smoker_C3


title: MESA_nonsmoker_H8

value: nonsmoker


title: MESA_nonsmoker_H2


title: MESA_smoker_D1


title: MESA_nonsmoker_H6


title: MESA_nonsmoker_G8


title: MESA_smoker_F7


title: MESA_nonsmoker_G6


title: MESA_nonsmoker_H4


title: BT549 Ctrl B

value: untreated, 48 hours


title: MESA_nonsmoker_G10


title: BT549 miR-200c B


title: MESA_smoker_D5


title: BT549 Ctrl C


title: MESA_nonsmoker_F6


title: MESA_nonsmoker_F8


title: MESA_nonsmoker_G2


title: MESA_nonsmoker_F4


title: MESA_nonsmoker_F2


title: MESA_nonsmoker_D8


title: MESA_nonsmoker_D6


title: MESA_nonsmoker_G4


title: MESA_nonsmoker_D4


title: MESA_nonsmoker_F10


title: MESA_nonsmoker_E8


title: MESA_nonsmoker_E6


title: MESA_nonsmoker_E2


title: MESA_nonsmoker_C2


title: MESA_nonsmoker_C6


title: MESA_nonsmoker_D2


title: BT549 Ctrl A


title: BT549 miR-200c C


title: MESA_nonsmoker_C8


title: MESA_nonsmoker_C10


title: MESA_nonsmoker_D10


title: MESA_nonsmoker_C4


title: hip_lt_age_rep1

city: Lexington

first: Eric

middle: M

last: Blalock

state: KY

address: 800 Rose St.

department: Molecular and Biomedical Pharmacology

institute: University of Kentucky

description: Gene expression data from aged viral FKBP1b hippocampus, injected at age 12 months, assayed at 21 months (long term- 9 month- exposure)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G scanner

data_processing: The data were analyzed with Partek software using the Robust Multi-Array (RMA) algorithm with default analysis settings

organism: Rattus norvegicus

source_name: hippocampus, aged long term (LT) FKBP1b treatment

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: age (mo)

value: 21 months old

value: male

value: hippocampus

value: AAV FKBP1b LT

tag: rin


title: hip_ctrl_age_rep4

description: Gene expression data from aged viral vector control hippocampus, injected at age 18 months, assayed at 21 months (short term- 3 month- exposure)

source_name: hippocampus, aged control

value: AAV GFP ST


title: hip_st_age_rep6

description: Gene expression data from aged viral FKBP1b hippocampus, injected at age 18 months, assayed at 21 months (short term- 3 month- exposure)

source_name: hippocampus, aged short term (ST) FKBP1b treatment

value: AAV FKBP1b ST


title: hip_st_age_rep3


title: hip_lt_age_rep2


title: hip_lt_age_rep4


title: hip_lt_age_rep3


title: hip_st_age_rep2


title: hip_lt_age_rep6


title: hip_lt_age_rep5


title: hip_st_age_rep5


title: hip_st_age_rep4


title: hip_ctrl_yng_rep1

description: Gene expression data from young control rat dorsal hippocampus

source_name: hippocampus, young control

value: 5-6 months old

value: sham


title: hip_ctrl_age_rep3


title: hip_ctrl_yng_rep2


title: hip_ctrl_age_rep5


title: hip_st_age_rep1


title: hip_ctrl_yng_rep4


title: hip_ctrl_age_rep2


title: hip_ctrl_yng_rep3


title: hip_ctrl_age_rep1


title: hip_ctrl_yng_rep5


title: WK12_TG_ND_Dorsal root ganglion_rep 4

city: Gainesville

first: VIJAYENDRAN

last: CHANDRAN

state: FL

address: Assistant Professor, Department of Pediatrics,  University of Florida, School of Medicine, 1600 SW Archer Road, Box 100296

institute: University of Florida

description:
replicate 4
X_9985525042_A

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

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

extract_protocol:
miRNeasy mini kit (Qiagen)
Total RNA was extracted using the miRNeasy mini kit (Qiagen) according to manufacturer’s protocol and including an on-column DNase digest (RNase free DNAse set; Qiagen). RNA samples were immediately aliquoted and stored at -80°C. RNA concentration and integrity were later determined using a Nanodrop Spectrophotometer (ThermoFisher Scientific) and TapeStation 2200 (Agilent Technologies), respectively.

treatment_protocol: Mouse was sacrificed by cervical dislocation and tissue was dissected and rinsed in cold PBS quickly (3X) to remove blood. Tissue samples were transferred immediately into 2 mL RNase-free tubes and immersed into liquid nitrogen. The collected tissue was stored in -80°C freezer immediately.

tag: age

value: 3-4 months

tag: genotype/variation

value: Fxn deficiency (FRDAkd)

tag: treated with

value: No Dox

tag: time point

value: Week 12

value: Dorsal root ganglion


title: WK12_TG_ND_Dorsal root ganglion_rep 3

description:
replicate 3
X_9985525039_H

tag: strain background


title: WK16_TG_ND_Dorsal root ganglion_rep 4

description:
replicate 4
X_9985525042_D

value: Week 16

tag: tissue


title: WK16_WT_Dox_Dorsal root ganglion_rep 3

description:
replicate 3
X_9985525042_G

value: wild type

value: Dox


title: WK12_WT_Dox_Dorsal root ganglion_rep 4

description:
replicate 4
X_9985525042_F


title: WK16_TG_Dox_Dorsal root ganglion_rep 4

description:
replicate 4
X_9985525042_C


title: WK0_TG_Dox_Dorsal root ganglion_rep 4

description:
replicate 4
X_9985525042_E

value: Week 0


title: WK4R_TG_DoxR_Dorsal root ganglion_rep 4

description:
replicate 4
X_9985525042_H

value: Dox Rescue

value: Week 4 Rescue


title: WK16_TG_Dox_Dorsal root ganglion_rep 3

description:
replicate 3
X_9985525039_D


title: WK20_TG_Dox_Dorsal root ganglion_rep 4

description:
replicate 4
X_9985525042_B

value: Week 20


title: WK20_WT_Dox_Dorsal root ganglion_rep 3

description:
replicate 3
X_9985525039_A


title: WK8R_TG_DoxR_Dorsal root ganglion_rep 4

description:
replicate 4
X_9985525035_H

value: Week 8 Rescue


title: WK3_TG_Dox_Dorsal root ganglion_rep 4

description:
replicate 4
X_9985525039_B

value: Week 3


title: WK0_TG_ND_Dorsal root ganglion_rep 4

description:
replicate 4
X_9985525039_E


title: MESA_smoker_E1

tag: cell type

value: primary circulating CD14+ cells

value: smoker

value: MESA


title: WK3_TG_ND_Dorsal root ganglion_rep 4

description:
replicate 4
X_9985525039_F

value: 3-4 months


title: WK8R_TG_DoxR_Dorsal root ganglion_rep 3

description:
replicate 3
X_9982502086_E

value: Fxn deficiency (FRDAkd)


title: WK12_TG_Dox_Dorsal root ganglion_rep 4

description:
replicate 4
X_9982502086_F


title: WK0_TG_ND_Dorsal root ganglion_rep 3

description:
replicate 3
X_9985525035_C

value: No Dox


title: WK20_TG_Dox_Dorsal root ganglion_rep 3

description:
replicate 3
X_9985525035_E


title: WK16_TG_Dox_Dorsal root ganglion_rep 2

description:
replicate 2
X_9985525035_G


title: WK12_WT_Dox_Dorsal root ganglion_rep 3

description:
replicate 3
X_9985525039_G

value: Week 12


title: WK20_TG_ND_Dorsal root ganglion_rep 4

description:
replicate 4
X_9985525035_D

value: Dorsal root ganglion


title: WK16_WT_Dox_Dorsal root ganglion_rep 2

description:
replicate 2
X_9985525035_B

value: Week 16


title: WK3_TG_Dox_Dorsal root ganglion_rep 3

description:
replicate 3
X_9985525035_F


title: WK3_TG_ND_Dorsal root ganglion_rep 3

description:
replicate 3
X_9985525035_A


title: WK0_TG_Dox_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502086_H


title: WK0_TG_Dox_Dorsal root ganglion_rep 3

description:
replicate 3
X_9985525039_C


title: WK0_WT_Dox_Dorsal root ganglion_rep 3

description:
replicate 3
X_9982502086_C

value: wild type


title: WK12_TG_Dox_Dorsal root ganglion_rep 3

description:
replicate 3
X_9982502086_A

value: Dox


title: WK3_TG_Dox_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502086_B


title: WK20_TG_Dox_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502086_D


title: WK16_TG_ND_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502081_B


title: WK4R_TG_DoxR_Dorsal root ganglion_rep 3

description:
replicate 3
X_9982502081_C


title: WK3_TG_ND_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502081_D


title: WK3_WT_Dox_Dorsal root ganglion_rep 3

description:
replicate 3
X_9982502059_F


title: WK12_WT_Dox_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502081_E


title: WK20_TG_ND_Dorsal root ganglion_rep 3

description:
replicate 3
X_9982502081_A


title: WK8R_TG_DoxR_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502081_H


title: WK16_TG_ND_Dorsal root ganglion_rep 3

description:
replicate 3
X_9982502081_G


title: WK4R_TG_DoxR_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502059_G


title: WK20_TG_Dox_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502059_H


title: WK0_WT_Dox_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502081_F

value: Week 0


title: WK20_TG_ND_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502059_D


title: WK3_TG_Dox_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502053_E


title: WK12_TG_ND_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502053_H


title: WK20_WT_Dox_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502059_B


title: WK20_TG_ND_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502053_C


title: WK20_WT_Dox_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502053_A


title: WK12_TG_Dox_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502059_E


title: WK12_TG_Dox_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502059_C


title: WK16_WT_Dox_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502053_D


title: WK0_WT_Dox_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502059_A


title: WK3_WT_Dox_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502053_G


title: WK16_TG_Dox_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502050_C


title: WK4R_TG_DoxR_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502050_D

value: Dox Rescue


title: WK12_TG_ND_Cerebellum_rep 4

description:
replicate 4
X_9985525051_B

value: Cerebellum


title: WK12_WT_Dox_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502050_H


title: WK0_TG_ND_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502053_B


title: WK8R_TG_DoxR_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502050_A


title: WK0_TG_Dox_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502050_G


title: WK20_TG_ND_Cerebellum_rep 4

description:
replicate 4
X_9993942036_B

value: Week 20


title: WK8R_TG_DoxR_Cerebellum_rep 4

description:
replicate 4
X_9985525051_F

value: Week 8 Rescue


title: WK16_TG_ND_Cerebellum_rep 4

description:
replicate 4
X_9993942036_C


title: WK20_TG_Dox_Cerebellum_rep 4

description:
replicate 4
X_9985525051_C


title: WK3_TG_ND_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502050_B

value: Week 3


title: WK4R_TG_DoxR_Cerebellum_rep 4

description:
replicate 4
X_9985525045_G

value: Week 4 Rescue


title: WK3_TG_ND_Cerebellum_rep 4

description:
replicate 4
X_9985525050_G


title: WK3_WT_Dox_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502050_F


title: WK3_TG_Dox_Cerebellum_rep 4

description:
replicate 4
X_9985525043_F


title: WK16_TG_ND_Dorsal root ganglion_rep 1

description:
replicate 1
X_9982502050_E


title: WK12_TG_Dox_Cerebellum_rep 4

description:
replicate 4
X_9993942036_H


title: WK0_TG_ND_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502053_F


title: WK12_WT_Dox_Cerebellum_rep 4

description:
replicate 4
X_9985525051_A


title: WK0_TG_Dox_Cerebellum_rep 4

description:
replicate 4
X_3998978014_D


title: WK16_WT_Dox_Cerebellum_rep 3

description:
replicate 3
X_9993942036_G


title: hip_ctrl_yng_rep6

tag: strain

value: 5-6 months old

tag: gender

value: male

value: hippocampus

value: sham


title: WK0_TG_ND_Cerebellum_rep 4

description:
replicate 4
X_9985525045_E

value: 3-4 months

value: Fxn deficiency (FRDAkd)

value: No Dox


title: WK0_WT_Dox_Cerebellum_rep 3

description:
replicate 3
X_9993942010_G


title: WK0_TG_ND_Cerebellum_rep 3

description:
replicate 3
X_9985525043_E


title: WK12_TG_ND_Cerebellum_rep 3

description:
replicate 3
X_9985525043_H

value: Week 12


title: WK16_TG_Dox_Cerebellum_rep 4

description:
replicate 4
X_3998978014_F

value: Week 16


title: WK12_TG_ND_Dorsal root ganglion_rep 2

description:
replicate 2
X_9982502086_G

value: Dorsal root ganglion


title: WK4R_TG_DoxR_Cerebellum_rep 3

description:
replicate 3
X_9985525043_C


title: WK3_TG_ND_Cerebellum_rep 3

description:
replicate 3
X_9985525043_A


title: WK20_TG_Dox_Cerebellum_rep 3

description:
replicate 3
X_9985525050_B

value: Dox


title: WK16_TG_ND_Cerebellum_rep 3

description:
replicate 3
X_3998978005_C


title: WK3_WT_Dox_Cerebellum_rep 3

description:
replicate 3
X_9985525051_E

value: wild type


title: WK4R_TG_DoxR_Cerebellum_rep 2

description:
replicate 2
X_3998978014_E

value: Dox Rescue

value: Cerebellum


title: WK0_TG_Dox_Cerebellum_rep 3

description:
replicate 3
X_3998978005_E

value: Week 0


title: WK20_WT_Dox_Cerebellum_rep 3

description:
replicate 3
X_9993942010_C

value: Week 20


title: WK12_TG_Dox_Cerebellum_rep 3

description:
replicate 3
X_3998978010_G


title: WK12_TG_ND_Cerebellum_rep 2

description:
replicate 2
X_3998978003_C


title: WK20_TG_ND_Cerebellum_rep 3

description:
replicate 3
X_3998978005_F


title: WK16_TG_Dox_Cerebellum_rep 3

description:
replicate 3
X_3998978003_B


title: WK12_WT_Dox_Cerebellum_rep 3

description:
replicate 3
X_3998945080_G


title: WK8R_TG_DoxR_Cerebellum_rep 3

description:
replicate 3
X_9985525045_B

value: Week 8 Rescue


title: WK3_TG_Dox_Cerebellum_rep 3

description:
replicate 3
X_3998945061_D

value: Week 3


title: WK12_TG_Dox_Cerebellum_rep 2

description:
replicate 2
X_3998978005_D


title: WK20_TG_ND_Cerebellum_rep 2

description:
replicate 2
X_3998978003_D


title: WK3_TG_ND_Cerebellum_rep 2

description:
replicate 2
X_3998978003_G


title: WK3_WT_Dox_Cerebellum_rep 2

description:
replicate 2
X_3998978005_A


title: WK20_TG_Dox_Cerebellum_rep 2

description:
replicate 2
X_3998978005_G


title: WK20_WT_Dox_Cerebellum_rep 2

description:
replicate 2
X_3998978010_C


title: WK0_WT_Dox_Cerebellum_rep 2

description:
replicate 2
X_9985525050_A


title: WK16_WT_Dox_Cerebellum_rep 2

description:
replicate 2
X_3998978014_A


title: WK8R_TG_DoxR_Cerebellum_rep 2

description:
replicate 2
X_3998945103_E


title: WK16_TG_ND_Cerebellum_rep 2

description:
replicate 2
X_3998945098_F


title: WK0_TG_ND_Cerebellum_rep 2

description:
replicate 2
X_3998945097_H


title: WK20_WT_Dox_Cerebellum_rep 1

description:
replicate 1
X_3998978005_H


title: WK0_TG_Dox_Cerebellum_rep 2

description:
replicate 2
X_3998945103_C


title: WK12_WT_Dox_Cerebellum_rep 2

description:
replicate 2
X_3998945061_E


title: WK3_TG_ND_Cerebellum_rep 1

description:
replicate 1
X_3998945103_F


title: WK20_TG_ND_Cerebellum_rep 1

description:
replicate 1
X_3998945097_F


title: WK16_WT_Dox_Cerebellum_rep 1

description:
replicate 1
X_3998945103_A


title: WK3_WT_Dox_Cerebellum_rep 1

description:
replicate 1
X_3998945103_B


title: WK0_WT_Dox_Cerebellum_rep 1

description:
replicate 1
X_3998978003_F


title: WK16_TG_Dox_Cerebellum_rep 2

description:
replicate 2
X_3998945098_C


title: WK12_TG_Dox_Cerebellum_rep 1

description:
replicate 1
X_3998945098_D


title: WK20_TG_Dox_Cerebellum_rep 1

description:
replicate 1
X_3998945098_H


title: WK0_TG_ND_Cerebellum_rep 1

description:
replicate 1
X_3998945061_H


title: WK4R_TG_DoxR_Cerebellum_rep 1

description:
replicate 1
X_3998945097_A

value: Week 4 Rescue


title: WK12_TG_Dox_Heart_rep 4

description:
replicate 4
X_9993942010_F

value: Heart


title: WK16_WT_Dox_Heart_rep 3

description:
replicate 3
X_9993942036_F


title: WK3_TG_Dox_Cerebellum_rep 1

description:
replicate 1
X_3998945038_E


title: WK0_TG_Dox_Cerebellum_rep 1

description:
replicate 1
X_3998945080_A


title: WK16_TG_Dox_Cerebellum_rep 1

description:
replicate 1
X_3998945080_C


title: WK16_TG_ND_Cerebellum_rep 1

description:
replicate 1
X_3998945061_F


title: WK8R_TG_DoxR_Cerebellum_rep 1

description:
replicate 1
X_3998945080_H


title: WK16_TG_ND_Heart_rep 4

description:
replicate 4
X_9993942036_E


title: WK0_TG_ND_Heart_rep 4

description:
replicate 4
X_9993942010_H


title: WK8R_TG_DoxR_Heart_rep 4

description:
replicate 4
X_9993942036_D


title: WK20_TG_Dox_Heart_rep 4

description:
replicate 4
X_9993942036_A


title: WK12_TG_ND_Cerebellum_rep 1

description:
replicate 1
X_3998945038_G


title: WK12_WT_Dox_Cerebellum_rep 1

description:
replicate 1
X_3998945061_B


title: WK3_TG_Dox_Cerebellum_rep 2

description:
replicate 2
X_3998945061_A


title: WK3_WT_Dox_Heart_rep 3

description:
replicate 3
X_9993942010_A


title: WK12_TG_Dox_Heart_rep 3

description:
replicate 3
X_9993942010_E


title: WK16_WT_Dox_Heart_rep 2

description:
replicate 2
X_9993942010_D


title: WK3_TG_ND_Heart_rep 4

description:
replicate 4
X_9985525051_H


title: WK3_TG_ND_Heart_rep 3

description:
replicate 3
X_9985525045_F


title: WK20_TG_ND_Heart_rep 4

description:
replicate 4
X_9993942010_B


title: WK0_TG_ND_Heart_rep 3

description:
replicate 3
X_9985525051_D


title: WK3_WT_Dox_Heart_rep 2

description:
replicate 2
X_9985525051_G


title: WK8R_TG_DoxR_Heart_rep 3

description:
replicate 3
X_9985525050_C


title: WK20_TG_Dox_Heart_rep 3

description:
replicate 3
X_9985525045_D


title: WK0_WT_Dox_Heart_rep 2

description:
replicate 2
X_9985525045_C


title: WK3_TG_Dox_Heart_rep 4

description:
replicate 4
X_9985525050_E


title: WK16_TG_ND_Heart_rep 3

description:
replicate 3
X_9985525045_A


title: WK12_TG_ND_Heart_rep 4

description:
replicate 4
X_9985525045_H


title: WK20_TG_ND_Heart_rep 1

description:
replicate 1
X_3998978014_H


title: WK12_WT_Dox_Heart_rep 3

description:
replicate 3
X_3998978014_C


title: WK0_TG_Dox_Heart_rep 3

description:
replicate 3
X_3998978010_F


title: WK20_WT_Dox_Heart_rep 3

description:
replicate 3
X_9985525043_G


title: WK20_TG_ND_Heart_rep 2

description:
replicate 2
X_9985525050_D


title: WK4R_TG_DoxR_Heart_rep 4

description:
replicate 4
X_3998978014_B


title: WK3_TG_Dox_Heart_rep 3

description:
replicate 3
X_3998978010_E


title: WK16_TG_ND_Heart_rep 1

description:
replicate 1
X_3998978010_D


title: WK12_WT_Dox_Heart_rep 4

description:
replicate 4
X_3998978014_G


title: WK4R_TG_DoxR_Heart_rep 3

description:
replicate 3
X_3998978005_B


title: WK0_WT_Dox_Heart_rep 3

description:
replicate 3
X_9985525050_F


title: WK16_TG_Dox_Heart_rep 2

description:
replicate 2
X_3998978003_H


title: WK16_TG_Dox_Heart_rep 3

description:
replicate 3
X_3998978010_A


title: WK20_TG_Dox_Heart_rep 2

description:
replicate 2
X_3998978010_H


title: WK16_TG_ND_Heart_rep 2

description:
replicate 2
X_9985525043_B


title: WK20_TG_ND_Heart_rep 3

description:
replicate 3
X_9985525050_H


title: WK16_TG_Dox_Heart_rep 4

description:
replicate 4
X_3998978010_B


title: WK8R_TG_DoxR_Heart_rep 2

description:
replicate 2
X_3998978003_E


title: WK3_TG_Dox_Heart_rep 2

description:
replicate 2
X_3998978003_A


title: WK0_TG_ND_Heart_rep 2

description:
replicate 2
X_3998945103_D


title: WK12_TG_ND_Heart_rep 2

description:
replicate 2
X_3998945097_E


title: WK4R_TG_DoxR_Heart_rep 2

description:
replicate 2
X_3998945098_E


title: WK0_WT_Dox_Heart_rep 1

description:
replicate 1
X_3998945080_F


title: WK0_TG_Dox_Heart_rep 4

description:
replicate 4
X_9985525043_D


title: WK12_TG_Dox_Heart_rep 2

description:
replicate 2
X_3998945103_H


title: WK8R_TG_DoxR_Heart_rep 1

description:
replicate 1
X_3998945097_B


title: WK3_TG_Dox_Heart_rep 1

description:
replicate 1
X_3998945097_C


title: WK0_TG_Dox_Heart_rep 2

description:
replicate 2
X_3998945103_G


title: WK3_TG_ND_Heart_rep 2

description:
replicate 2
X_3998945080_B


title: WK12_TG_ND_Heart_rep 1

description:
replicate 1
X_3998945097_D


title: WK16_TG_Dox_Heart_rep 1

description:
replicate 1
X_3998945038_F


title: WK12_TG_ND_Heart_rep 3

description:
replicate 3
X_3998945098_G


title: WK20_WT_Dox_Heart_rep 2

description:
replicate 2
X_3998945098_B


title: WK12_WT_Dox_Heart_rep 1

description:
replicate 1
X_3998945038_H


title: WK0_TG_ND_Heart_rep 1

description:
replicate 1
X_3998945098_A


title: WK12_WT_Dox_Heart_rep 2

description:
replicate 2
X_3998945080_D


title: WK12_TG_Dox_Heart_rep 1

description:
replicate 1
X_3998945061_C


title: WK0_TG_Dox_Heart_rep 1

description:
replicate 1
X_3998945038_D


title: WK20_TG_Dox_Heart_rep 1

description:
replicate 1
X_3998945097_G


title: WK20_WT_Dox_Heart_rep 1

description:
replicate 1
X_3998945061_G


title: Liver H8 rep1 part 2

city: Dalian

first: Zhou

last: Zhang

state: Liaoning

address: Linggong Road 2

department: Environmental Science and Technology

country: China

institute: Dalian University of Technology

description: Gene expression after 96h exposure of surface water from site H8

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent Technologies, CA) in Hybridization Oven (Agilent Technologies, CA). After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, MA) with Gene Expression Wash Buffer Kit (Agilent Technologies, CA).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software 11.0 (Agilent Technologies, CA) was used to analyze the raw data, which are normalized by Quantile algorithm.

organism: Danio rerio

source_name: liver, 97h, site H8

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies, CA).

growth_protocol: Zebrafish were raised at 27±1℃ with a 14:10 h light/dark cycle.

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

treatment_protocol: Adult zebrafish were treated with surface water from several sites of the Hun River for 96h.

value: liver

value: male

value: 3 month


title: WK16_WT_Dox_Heart_rep 1

description:
replicate 1
X_3998945038_C

value: 3-4 months


title: WK4R_TG_DoxR_Heart_rep 1

description:
replicate 1
X_3998945080_E

value: Fxn deficiency (FRDAkd)


title: Liver X rep1 part 2

description: Gene expression after 96h exposure of surface water from site X

source_name: liver, 97h, site X


title: WK3_TG_ND_Heart_rep 1

description:
replicate 1
X_3998945038_A

value: No Dox


title: WK3_WT_Dox_Heart_rep 1

description:
replicate 1
X_3998945038_B


title: Liver H4 rep1 part 2

description: Gene expression after 96h exposure of surface water from site H4

source_name: liver, 96h, site H4


title: Liver H1 rep1 part 2

description: Gene expression after 96h exposure of surface water from site H1

source_name: liver, 96h, site H1


title: Liver control rep1 part 2

description: Gene expression after 96h untreated

source_name: liver, 96h, control


title: Liver H3 rep1 part 2

description: Gene expression after 96h exposure of surface water from site H3

source_name: liver, 96h, site H3


title: Gpr97 deficiency - Ischemia/reperfusion injury 640

city: Jinan

first: Wei

last: Fang

address: Wenhua Xi Road 44#

institute: Shandong university

description: Gene expression of kidney from  renal IRI injuried Gpr97 deficiency mice

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)

treatment_protocol: Fresh tisuues of kidney from wide type mice and Gpr97 deficiency mice with or without renal IRI injury

value: Ischemia/reperfusion injury

value: kidney

tag: genotype

value: Gpr97 deficiency


title: Liver H2 rep1 part 2

description: Gene expression after 96h exposure of surface water from site H2

source_name: liver, 96h, site H2


title: Liver H5 rep1 part 2

description: Gene expression after 96h exposure of surface water from site H5

source_name: liver, 96h, site H5


title: wild type Ischemia/reperfusion injury 11

description: Gene expression of kidney from  renal IRI injuried wild type mice

value: wild type


title: wild type sham-operated 949

description: Gene expression of kidney from sham-operated wild type mice

value: sham


title: wild type Ischemia/reperfusion injury 929

source_name: kidney from renal IRI injuried wild type mice


title: Gpr97 deficiency - sham-operated 238

description: Gene expression of kidney from sham-operated Gpr97 deficiency mice


title: blood,MAP,Post-treatment A#726-M029-G

city: Singapore

first: Ene Choo

last: Tan

address: 100 Bukit Timah Road

department: KKRC

country: Singapore

institute: KK Women's & Children's Hospital

description:
Gene expression data from Post-treatment of MAP group
GLOBINclear RNA

hyb_protocol: Following fragmentation, 11 ug of fragmented and labeled cRNA was hybridized for 16 hr at 45˚C on GeneChip Human Genome U133 Plus 2.0 array. Arrays were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip 3000 7G with autoloader. The images were analyzed using Affymetrix GeneChip Command Console version 4.3.2 and metric analysis were carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console 1.4.1.46.

data_processing: Data were analyzed with Microarray Suite 5 (MAS5) and Robust Multi-array Average (RMA) using Affymetrix Expression Console 1.4.1.46. Affymetrix default analysis settings were used. In the addition, the correction for batch and gender effects was performed with ANCOVA.

source_name: blood,MAP,Post-treatment

label_protocol: Biotinylated cRNA were prepared according to the GeneChip 3’ IVT PLUS Reagent Kit protocol from 100 ng of GLOBINclear RNA.

growth_protocol: 1-3ml blood was collected using Tempus Blood RNA tubes from each subject.The blood tubes were stored in the freezer at -80˚C until further processed (at baseline and 9 months).

extract_protocol: Total RNA was isolated using Tempus Spin RNA Isolation Kit. Globin mRNA was depleted from total RNA using the GLOBINclear Kit.

treatment_protocol: Blood samples from both groups were extracted in batches.

tag: group

value: MAP

value: Post

value: Female

tag: race

value: Chinese

tag: rna integrity number (rin)


title: blood,MAP,Post-treatment A#484-M011-G


title: blood,MAP,Post-treatment A#688-M052-G


title: wild type sham-operated 9

source_name: kidney from sham-operated wild type mice


title: blood,MAP,Post-treatment A#545-M026-G


title: blood,MAP,Post-treatment A#617-M047-G


title: blood,MAP,Post-treatment A#543-M038-G

value: Male


title: blood,MAP,Post-treatment A#631-M032-G


title: blood,MAP,Post-treatment A#430-M016-G


title: blood,MAP,Post-treatment A#429-M010-G


title: blood,MAP,Post-treatment A#317-M036-G


title: blood,MAP,Post-treatment A#395-M028-G


title: blood,MAP,Pre-treatment E#732-M054-G

description:
Gene expression data from Pre-treatment of MAP group
GLOBINclear RNA

source_name: blood,MAP,Pre-treatment

value: Pre


title: blood,MAP,Post-treatment A#477-M053-G


title: blood,MAP,Post-treatment A#457-M050-G


title: blood,MAP,Pre-treatment E#726-M029-G


title: blood,MAP,Pre-treatment E#699-M027-G


title: blood,MAP,Post-treatment A#321-M004-G


title: blood,MAP,Pre-treatment E#688-M052-G


title: blood,MAP,Post-treatment A#656-M007-G


title: blood,MAP,Post-treatment A#447-M040-G


title: blood,MAP,Pre-treatment E#617-M047-G


title: blood,MAP,Pre-treatment E#698-M035-G


title: blood,MAP,Pre-treatment E#631-M032-G


title: blood,MAP,Post-treatment A#061-M018-G


title: blood,MAP,Pre-treatment E#656-M007-G


title: blood,MAP,Pre-treatment E#545-M026-G


title: blood,MAP,Pre-treatment E#447-M040-G


title: blood,MAP,Pre-treatment E#543-M038-G


title: blood,MAP,Pre-treatment E#506-M051-G

value: Indian


title: blood,MAP,Pre-treatment E#463-M005-G


title: blood,MAP,Pre-treatment E#484-M011-G


title: blood,MAP,Pre-treatment E#429-M010-G


title: blood,MAP,Pre-treatment E#457-M050-G


title: blood,MAP,Pre-treatment E#395-M028-G


title: blood,MAP,Pre-treatment E#430-M016-G


title: blood,MAP,Pre-treatment E#321-M004-G


title: blood,MAP,Pre-treatment E#477-M053-G


title: blood,MAP,Pre-treatment E#317-M036-G


title: blood,MAP,Pre-treatment E#135-M042-G


title: blood,MAP,Pre-treatment E#061-M018-G


title: blood,HEP,Post-treatment A#665-M034-G

description:
Gene expression data from Post-treatment of HEP group
GLOBINclear RNA

source_name: blood,HEP,Post-treatment

value: HEP


title: blood,HEP,Post-treatment A#660-M012-G


title: blood,MAP,Pre-treatment E#263-M055-G


title: blood,HEP,Post-treatment A#729-M006-G


title: blood,MAP,Pre-treatment E#306-M013-G


title: blood,HEP,Post-treatment A#672-M001-G


title: blood,HEP,Post-treatment A#701-M002-G


title: blood,HEP,Post-treatment A#536-M044-G


title: blood,HEP,Post-treatment A#565-M017-G


title: blood,HEP,Post-treatment A#712-M021-G


title: blood,HEP,Post-treatment A#564-M041-G


title: blood,HEP,Post-treatment A#075-M030-G


title: blood,HEP,Pre-treatment E#738-M022-G

description:
Gene expression data from Pre-treatment of HEP group
GLOBINclear RNA

source_name: blood,HEP,Pre-treatment


title: blood,HEP,Post-treatment A#738-M022-G


title: blood,HEP,Post-treatment A#143-M043-G


title: blood,HEP,Pre-treatment E#701-M002-G


title: blood,HEP,Pre-treatment E#729-M006-G


title: blood,HEP,Post-treatment A#542-M039-G


title: blood,HEP,Post-treatment A#428-M015-G


title: blood,HEP,Post-treatment A#141-M046-G


title: blood,HEP,Post-treatment A#462-M031-G


title: blood,HEP,Post-treatment A#474-M025-G


title: blood,HEP,Post-treatment A#524-M045-G


title: blood,MAP,Pre-treatment E#013-M014-G


title: blood,HEP,Post-treatment A#410-M009-G


title: blood,HEP,Pre-treatment E#564-M041-G


title: blood,HEP,Pre-treatment E#663-M003-G


title: blood,HEP,Pre-treatment E#607-M023-G


title: blood,HEP,Pre-treatment E#665-M034-G


title: blood,HEP,Pre-treatment E#672-M001-G


title: blood,HEP,Pre-treatment E#712-M021-G


title: blood,HEP,Pre-treatment E#348-M019-G


title: blood,HEP,Pre-treatment E#542-M039-G


title: blood,HEP,Pre-treatment E#120-M024-G


title: blood,HEP,Pre-treatment E#143-M043-G


title: blood,HEP,Pre-treatment E#524-M045-G


title: blood,HEP,Pre-treatment E#536-M044-G


title: blood,HEP,Pre-treatment E#565-M017-G


title: C3: Normozoospermic fertile control subject

type: genomic

city: Ribeirão Preto

first: Juliana

middle: Dourado

last: Grzesiuk

state: São Paulo

address: Avenida Bandeirantes, 3900

department: Genetics

country: Brazil

institute: USP

hyb_protocol: Samples were hybridized on the array slides for 24h at 67°C and 20rpm in the hybridization oven.

scan_protocol: The samples were scanned using the DNA microarray scanner SureScan B Scanner (Agilent), and The Feature Extraction software (version 12.0, Agilent Technologies) was used for the analysis of the scanned slide image results.

data_processing: The extracted data were interpreted by software Nexus 8.0 using the Fast Adaptive States Segmentation Technique (FASST2)

source_name: Normozoospermic fertile control peripheral blood

label_protocol: 1µg genomic DNA was fragmented with AluI and RsaI restriction enzymes and subsequently labeled with Cy5-dCTP (for the study samples) or Cy3-dCTP (for the Agilent Human Male Reference DNA) using a Genomic DNA Enzymatic Labeling Kit (Agilent, USA).

extract_protocol: Genomic DNA was extracted from peripheral blood using the MasterPureTM Complete DNA and RNA Purification Kit – Epicentre (US) following manufacturer's instructions

value: Peripheral blood

source_name: Comercial Male DNA reference from Agilent (#5190-4240)


title: blood,HEP,Pre-treatment E#474-M025-G


title: blood,HEP,Pre-treatment E#141-M046-G


title: blood,HEP,Pre-treatment E#660-M012-G


title: blood,HEP,Pre-treatment E#541-M037-G


title: C4: Normozoospermic fertile control subject


title: C6: Normozoospermic fertile control subject


title: blood,HEP,Pre-treatment E#462-M031-G


title: C1: Normozoospermic fertile control subject


title: blood,HEP,Pre-treatment E#075-M030-G


title: blood,HEP,Pre-treatment E#428-M015-G


title: C2: Normozoospermic fertile control subject


title: C5: Normozoospermic fertile control subject


title: 11S: Patient with severe oligozoospermia

source_name: Oligozoospermic peripheral blood


title: CRU_smoker_F092

source_name: human CD14+ cells from adult peripheral blood

value: primary circulating CD14+ cells

tag: smoking status

value: smoker

tag: population

value: CRU


title: 17E: Patient with extreme oligozoospermia


title: 18E: Patient with extreme oligozoospermia


title: blood,HEP,Pre-treatment E#486-M033-G

tag: treatment


title: CRU_smoker_F083


title: 9S: Patient with severe oligozoospermia


title: CRU_smoker_F062


title: 13E: Patient with extreme oligozoospermia


title: CRU_smoker_F040


title: CRU_smoker_F030


title: 1M: Patient with moderate oligozoospermia


title: 8S: Patient with severe oligozoospermia


title: 12E: Patient with extreme oligozoospermia


title: ox-6

city: Eugene

first: Patrick

middle: C

last: Phillips

state: OR

address: 272 Onyx Bridge 5289 University of Oregon

department: Biology

institute: University of Oregon

library_source: transcriptomic

data_processing:
Base-calls were performed using Illumina software
Initial processing was performed using the process_shortreads component of Stacks. In short, reads were demultiplexed, and the barcodes were removed. Reads with ambiguous barcodes were rescued if there were fewer than 2 mismatches, and discarded otherwise. Reads failing the Illumina chastity filter were also removed.
Filtered reads were aligned to the C. remanei genome using GSNAP version 2013-03-31 with parameters -N 1 -s -w 10000 --pairmax-RNA 10000
Reads aligning to genes were counted using htseq-count with parameters -m union -s no
Genome_build: LFJK02000000
Supplementary_files_format_and_content: tab-delimited text files with read counts per gene

molecule: polyA RNA

organism: Caenorhabditis remanei

source_name: pooled L1 tissue

growth_protocol: Worms were maintained on NGM-lite seeded with E. coli strain OP50 at 20°C

extract_protocol:
Approximately 100,000 individuals per replicate were flash frozen in Trizol. Total RNA was extracted using a standard Trizol extraction protocol. Poly-A mRNA was isolated from total RNA using the Dynabeads mRNA purification kit (Ambion).
mRNA was sheared to 200-600nt fragments using a buffered zinc solution (RNA fragmentation kit; Ambion). cDNA was synthesized from fragments using Superscript III, and barcoded sequencing adaptors were added to enable multiplexing of samples.

treatment_protocol: Populations were age-synchronized during the embryonic stage via a standard bleaching procedure. Embryos were incubated at either 20°C or 30°C in liquid buffer without food for 20 hours. Pooled L1 larvae were passed through a 20 micron filter immediately prior to tissue collection.

value: Oxidative-selected, derived from PX443

tag: developmental stage


title: ox-5


title: CRU_smoker_F072


title: ox-4


title: 16E: Patient with extreme oligozoospermia

tag: age


title: 10S: Patient with severe oligozoospermia


title: 15E: Patient with extreme oligozoospermia


title: CRU_smoker_F058


title: CRU_smoker_F048


title: 6S: Patient with severe oligozoospermia


title: 4M: Patient with moderate oligozoospermia


title: CRU_smoker_F068


title: CRU_smoker_F063


title: 7S: Patient with severe oligozoospermia


title: 2M: Patient with moderate oligozoospermia


title: CRU_nonsmoker_F105

value: nonsmoker


title: 14E: Patient with extreme oligozoospermia


title: 5S: Patient with severe oligozoospermia


title: CRU_smoker_F057


title: CRU_smoker_F028


title: CRU_nonsmoker_F085


title: CRU_smoker_F018


title: CRU_smoker_F031


title: CRU_smoker_F037


title: CRU_smoker_F011


title: CRU_smoker_F016


title: heat-8

value: Heat-selected, derived from PX443


title: CRU_smoker_F007


title: ox-2


title: 15-48_CO_DNP1 15-48/CO green

city: Orient

first: James

middle: J.

last: Zhu

department: Foreign Animal Disease Research Unit

institute: USDA-ARS

hyb_protocol: Cy3- and Cy5-labeled DNA from two tissue samples was hybridized to paired arrays in a dye-swap arrangement, for a total of four tissue samples per slide, using the Hi-RPM Gene Expression Hybridization Kit (cat. no. 5190-0404, Agilent) The slide assemblies were incubated for 18 hours at 65°C in a rotating oven set to 10 revolutions per minute. After the hybridization, array slides were washed following the manufacturer’s recommendations and coated with Cy5-stabilization and drying solution (cat. no. 5185-5979; Agilent).

scan_protocol: Washed and coated arrays were scanned immediately with a GenePix 4000B scanner (Molecular Devices). Each array image underwent thorough visual inspection to find and eliminate artifacts. Array features were then extracted with GenePix Pro 7.2 using standard settings.

data_processing: The median foreground and neighborhood background intensities for all arrays were extracted from the GenePix results files using the limma software package in the R/Bioconductor statistical environment. The feature background was corrected using the “normexp” method, which fits a convolution of normal and exponential distributions to the foreground intensities with the background intensities as a covariate. The expected signal given the observed foreground was used as the corrected intensity. This results in a smooth monotonic transformation of the background-subtracted intensities with positive corrected values. A small offset (+10) was applied to the intensities before log-transforming to shrink log-ratios towards zero at the lower intensities and avoid fanning. Log-ratios within each array were normalized for dye-bias to remove systematic trends. For each array, the log-ratios were adjusted using robustly fitted 5-parameter splines with high breakdown point regression and empirical Bayes shrinkage. Quantile normalization was then used to achieve consistency between arrays, i.e. ensure that the average intensities have the same empirical distribution across arrays leaving the log-ratios unchanged. The values in the matrix table are the signal intensities of all 45220 features on the array after quantile normalization. Using these signal intensities, a separate-channel approach using a common correlation model was used to analyze the two-color array data. The probes were not pre-filtered. For each of the 43768 bovine transcriptome and FMDV genome probes, the intra-spot correlation between the channels was estimated across all arrays and used to fit a linear model to the data in terms of the individual log-intensities. Once the linear model was fitted, inference proceeded in the same way as it would for log-ratios in a fully connected experimental design. Contrast matrices were set up for six comparisons, (i) between the temporally aligned paired groups of FMDV-infected animals (transitional carriers vs. transitional terminators and carriers vs. non-carriers), and (ii) between each of the four animal categories and the uninfected controls. For each contrast and probe, log2 fold changes of signal intensity and p-values were calculated. To account for multiple testing within a contrast, p-values were adjusted using the Y. Benjamini and Y. Hochberg (30) method to control the false-discovery rate (FDR). Values adjusted with this method are bounds on the FDR and are referred to as q-values. A q value of less than 0.05 was considered significant; accordingly, the expected proportion of false discoveries is controlled to be less than 5%. Accordingly, probes with q-values (adjusted p-values) >0.05 were removed from the output. Most of the subsequent analyses are based on the relative difference in signal intensity between transitional carriers and transitional terminators and between carriers and non-carriers. In these comparisons, probes that have higher signal intensity in transitional terminators or non-carriers have positive log2FC values; negative values indicate probes that had higher signal intensities in transitional carriers or carriers. Probes were ranked by log2FC, and only the top and bottom 0.1% of probes (i.e., the most strongly up- or downregulated probes) were further examined.

organism: Bos taurus

label_protocol: The extracted RNA was amplified by with the REPLI-g whole-transcriptome amplification single-cell kit (#150063, Qiagen) following the manufacturer’s instructions. Amplified DNA was purified using Agencourt® AMPure® XP magnetic beads (cat. no. A63880, Beckman Coulter, Indianapolis, USA) and fragmented by heating to 95°C for 30 minutes. Fragmented DNA was labeled with cyanine (Cy) 3- and 5 using the SureTag DNA labeling kit (cat. no. 5190-3400, Agilent) and purified with 30K Amicon cartridges.

extract_protocol: Follicle-associated epithelium (FAE) was retrieved from 10 µm cryosections using an Arcturus XT ™ LCM system. Dissected samples with a combined surface area of approximately 400.000 µm2 were captured onto individual CapSure Macro LCM caps (LCM0211, Life Technologies) which were immediately mounted onto micro-tubes containing 50µl of RNA extraction buffer (PicoPure™). RNA extraction was performed using the PicoPure™ RNA isolation kit (KIT0202, Life Technologies) with a final elution volume of 12µl. Total RNA quantity was determined using a NanoDrop 1000 spectrophotometer (Thermo Scientific) with RNA purity assessed by measurement of the A260/A280 ratio. FMDV RNA content in micro-dissected tissue samples was determined by RT-qPCR.

treatment_protocol: Twelve Holstein cattle were challenged by intranasopharyngeal deposition of 10^5 infectious doses of FMDV strain A24 Cruzeiro. Three additional non-vaccinated non-challenged animals were housed separately and used as negative controls. FMDV carrier status was determined by real-time RT-PCR analysis and virus isolation (VI) of oropharyngeal fluids (OPF) collected with a probang cup or of nasopharyngeal tissues collected at necropsy. Animals were euthanized by intravenous injection of sodium pentobarbital at various time points after infection, and nasopharyngeal epithelium was collected for laser-capture microdissection.

tag: persistence

value: uninfected controls


title: CRU_nonsmoker_F047


title: CRU_smoker_F001


title: heat-2


title: 15-15_NC_DSP1 15-15/NC green

value: non-carriers


title: 932_CO_DNP1 932/CO green


title: 14-32_NC_DNP1 14-32/NC green


title: CRU_nonsmoker_F044


title: 14-29_TT_DNP1 14-29/TT green

value: transitional terminators


title: heat-6


title: ox-3


title: CRU_nonsmoker_F075


title: heat-5


title: CRU_nonsmoker_F074


title: heat-7


title: ox-1


title: 14-54_CR_DSP2 14-54/CR green

value: carriers


title: CRU_nonsmoker_F073


title: CRU_nonsmoker_F033


title: 14-118_CR_DSP2 14-118/CR green


title: heat-4


title: heat-3


title: control20-7

value: Control selected, derived from PX443


title: 15-47_CO_DNP1 15-47/CO green


title: heat-1


title: CRU_nonsmoker_F082


title: 15-16_NC_DSP2 15-16/NC green


title: 14-30_CR_DSP2 14-30/CR green


title: CRU_nonsmoker_F081


title: control20-6


title: CRU_nonsmoker_F025


title: control20-4


title: 14-48_TT_DNP1 14-48/TT green


title: control20-3


title: control20-2


title: control20-1


title: CRU_nonsmoker_F049


title: 932_CO_DNP1 932/CO red


title: 14-08_TC_DSP2 14-08/TC green

value: transitional carriers


title: CRU_nonsmoker_F014


title: CRU_nonsmoker_F043


title: ancestor20-6


title: CRU_nonsmoker_F026


title: ancestor20-4


title: control20-5


title: CRU_nonsmoker_F017


title: 15-16_NC_DSP2 15-16/NC red


title: 14-54_CR_DSP2 14-54/CR red


title: 14-106_TC_DNP1 14-106/TC green


title: 14-30_CR_DSP2 14-30/CR red


title: control20-8


title: CRU_nonsmoker_F002


title: ancestor20-7


title: 3M: Patient with moderate oligozoospermia

value: Male


title: CRU_nonsmoker_F015


title: 14-108_NC_DNP1 14-108/NC green


title: 15-48_CO_DNP1 15-48/CO red


title: 14-28_TT_DNP1 14-28/TT red


title: ancestor20-8


title: ancestor20-3


title: 14-28_TT_DNP1 14-28/TT green


title: CRU_nonsmoker_F003


title: 15-15_NC_DSP1 15-15/NC red


title: 15-47_CO_DNP1 15-47/CO red


title: 14-48_TT_DNP1 14-48/TT red


title: liver_C57BLKS/J db/db mouse_rep3

city: Guangzhou

first: Yangzhi

last: Xu

address: No.250, Changgang East Road

department: Gastroenterology

institute: The Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou

description: hepatic gene expression of 8-week old db/db mouse

hyb_protocol: The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After extensive washing, the arrays were scanned by an Agilent G2505C Scanner.

data_processing: The Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. The GeneSpringGXv11.5.1 software package (Agilent Technologies) offered quantile normalization and background correction.

source_name: liver, C57BLKS/J  db/db mouse, replicate 3

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA was extracted from the liver of six mice (three NAFLD and control mice, each) using Trizol and treated with DNase I (Invitrogen, Carlsbad, CA). The integrity of RNA was assessed by electrophoresis on denatured agarose gel. Mouse LncRNA Microarray V2.0 (Arraystar, Rockville, MD) was used to study the profiles of mouse lncRNAs and protein-coding transcripts in the liver.

value: liver

value: female

value: 8 weeks

tag: background strain

value: db/db


title: liver_C57BLKS/J mouse_rep1

description: hepatic gene expression of 8-week old C57BLKS/J  mouse

source_name: liver, C57BLKS/J mouse, replicate 1

value: wildtype


title: 14-32_NC_DNP1 14-32/NC red


title: liver_C57BLKS/J  mouse_rep3

source_name: liver, C57BLKS/J  mouse, replicate 3


title: 14-10_TC_DSP2 14-10/TC green


title: ex-vivo_culture_timepoint_6_patient_ID:_Frozen10820_2010-2012_Kilifi_Kenya 10820_T6

status: Public on Dec 18 2017

first: Margaret

middle: Jane

last: Mackinnon

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).

organism: Plasmodium falciparum

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

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 6, Frozen10820, 2010-2012, Kilifi, Kenya, Low, 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_4_patient_ID:_Frozen10820_2010-2012_Kilifi_Kenya 10820_T4

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

value: ex-vivo culture, timepoint 4, Frozen10820, 2010-2012, Kilifi, Kenya, Low, Expt C


title: 14-29_TT_DNP1 14-29/TT red


title: ex-vivo_culture_timepoint_7_patient_ID:_Frozen10820_2010-2012_Kilifi_Kenya 10820_T7

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

value: ex-vivo culture, timepoint 7, Frozen10820, 2010-2012, Kilifi, Kenya, Low, Expt C


title: 14-10_TC_DSP2 14-10/TC red


title: liver_C57BLKS/J db/db mouse_rep2

source_name: liver, C57BLKS/J  db/db mouse, replicate 2

tag: tissue


title: 14-118_CR_DSP2 14-118/CR red


title: 14-108_NC_DNP1 14-108/NC red


title: 14-106_TC_DNP1 14-106/TC red


title: ex-vivo_culture_timepoint_3_patient_ID:_Frozen10820_2010-2012_Kilifi_Kenya 10820_T3

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

value: ex-vivo culture, timepoint 3, Frozen10820, 2010-2012, Kilifi, Kenya, Low, Expt C


title: liver_ C57BLKS/J db/db mouse_rep1

source_name: liver, C57BLKS/J  db/db mouse, replicate 1


title: ex-vivo_culture_timepoint_0_patient_ID:_Frozen10820_2010-2012_Kilifi_Kenya 10820_T0

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

value: ex-vivo culture, timepoint 0, Frozen10820, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_Frozen10761_2010-2012_Kilifi_Kenya 10761_T2

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

value: ex-vivo culture, timepoint 2, Frozen10761, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_Frozen10761_2010-2012_Kilifi_Kenya 10761_T1

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

value: ex-vivo culture, timepoint 1, Frozen10761, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_Frozen10820_2010-2012_Kilifi_Kenya 10820_T1

value: ex-vivo culture, timepoint 1, Frozen10820, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_Frozen10761_2010-2012_Kilifi_Kenya 10761_T0

value: ex-vivo culture, timepoint 0, Frozen10761, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_Frozen10760_2010-2012_Kilifi_Kenya 10760_T3

value: ex-vivo culture, timepoint 3, Frozen10760, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_Frozen10779_2010-2012_Kilifi_Kenya 10779_T0

value: ex-vivo culture, timepoint 0, Frozen10779, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_Frozen10761_2010-2012_Kilifi_Kenya 10761_T4

value: ex-vivo culture, timepoint 4, Frozen10761, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_Frozen10761_2010-2012_Kilifi_Kenya 10761_T3

value: ex-vivo culture, timepoint 3, Frozen10761, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_Frozen10779_2010-2012_Kilifi_Kenya 10779_T1

value: ex-vivo culture, timepoint 1, Frozen10779, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_Frozen10761_2010-2012_Kilifi_Kenya 10761_T5

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

value: ex-vivo culture, timepoint 5, Frozen10761, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_Frozen10760_2010-2012_Kilifi_Kenya 10760_T2

value: ex-vivo culture, timepoint 2, Frozen10760, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_Frozen10760_2010-2012_Kilifi_Kenya 10760_T7

value: ex-vivo culture, timepoint 7, Frozen10760, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_Frozen10820_2010-2012_Kilifi_Kenya 10820_T2

value: ex-vivo culture, timepoint 2, Frozen10820, 2010-2012, Kilifi, Kenya, Low, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_1_patient_ID:_Frozen10760_2010-2012_Kilifi_Kenya 10760_T1

value: ex-vivo culture, timepoint 1, Frozen10760, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_Frozen10760_2010-2012_Kilifi_Kenya 10760_T4

value: ex-vivo culture, timepoint 4, Frozen10760, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_Frozen10748_2010-2012_Kilifi_Kenya 10748_T5

value: ex-vivo culture, timepoint 5, Frozen10748, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_Frozen10615_2010-2012_Kilifi_Kenya 10615_T2

value: ex-vivo culture, timepoint 2, Frozen10615, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_Frozen10748_2010-2012_Kilifi_Kenya 10748_T0

value: ex-vivo culture, timepoint 0, Frozen10748, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_Frozen10738_2010-2012_Kilifi_Kenya 10738_T2

value: ex-vivo culture, timepoint 2, Frozen10738, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_Frozen10748_2010-2012_Kilifi_Kenya 10748_T4

value: ex-vivo culture, timepoint 4, Frozen10748, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_Frozen10748_2010-2012_Kilifi_Kenya 10748_T1

value: ex-vivo culture, timepoint 1, Frozen10748, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_3180_1994-1996_Kilifi_Kenya 3180_T5

value: ex-vivo culture, timepoint 5, 3180, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_Frozen10738_2010-2012_Kilifi_Kenya 10738_T4

value: ex-vivo culture, timepoint 4, Frozen10738, 2010-2012, Kilifi, Kenya, Low, Expt C


title: 14-08_TC_DSP2 14-08/TC red

value: transitional carriers


title: ex-vivo_culture_timepoint_3_patient_ID:_3180_1994-1996_Kilifi_Kenya 3180_T3

value: ex-vivo culture, timepoint 3, 3180, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1959_1994-1996_Kilifi_Kenya 1959_T7

value: ex-vivo culture, timepoint 7, 1959, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_Frozen10615_2010-2012_Kilifi_Kenya 10615_T5

value: ex-vivo culture, timepoint 5, Frozen10615, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1980_1994-1996_Kilifi_Kenya 1980_T1

value: ex-vivo culture, timepoint 1, 1980, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_3180_1994-1996_Kilifi_Kenya 3180_T0

value: ex-vivo culture, timepoint 0, 3180, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1980_1994-1996_Kilifi_Kenya 1980_T0

value: ex-vivo culture, timepoint 0, 1980, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_7_patient_ID:_Frozen10615_2010-2012_Kilifi_Kenya 10615_T7

value: ex-vivo culture, timepoint 7, Frozen10615, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1959_1994-1996_Kilifi_Kenya 1959_T6

value: ex-vivo culture, timepoint 6, 1959, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1959_1994-1996_Kilifi_Kenya 1959_T5

value: ex-vivo culture, timepoint 5, 1959, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1959_1994-1996_Kilifi_Kenya 1959_T4

value: ex-vivo culture, timepoint 4, 1959, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1980_1994-1996_Kilifi_Kenya 1980_T2

value: ex-vivo culture, timepoint 2, 1980, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_Frozen10738_2010-2012_Kilifi_Kenya 10738_T0

value: ex-vivo culture, timepoint 0, Frozen10738, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1958_1994-1996_Kilifi_Kenya 1958_T3

value: ex-vivo culture, timepoint 3, 1958, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_3180_1994-1996_Kilifi_Kenya 3180_T1

value: ex-vivo culture, timepoint 1, 3180, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_3180_1994-1996_Kilifi_Kenya 3180_T2

value: ex-vivo culture, timepoint 2, 3180, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1939_1994-1996_Kilifi_Kenya 1939_T6

value: ex-vivo culture, timepoint 6, 1939, 1994-1996, Kilifi, Kenya, High, Expt C


title: ancestor20-5


title: ex-vivo_culture_timepoint_7_patient_ID:_1915_1994-1996_Kilifi_Kenya 1915_T7

value: ex-vivo culture, timepoint 7, 1915, 1994-1996, Kilifi, Kenya, High, Expt C


title: liver_C57BLKS/J  mouse_rep2

source_name: liver, C57BLKS/J mouse, replicate 2

value: liver

value: female

value: 8 weeks

value: wildtype


title: ex-vivo_culture_timepoint_7_patient_ID:_1920_1994-1996_Kilifi_Kenya 1920_T7

value: ex-vivo culture, timepoint 7, 1920, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1958_1994-1996_Kilifi_Kenya 1958_T2

value: ex-vivo culture, timepoint 2, 1958, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_4_patient_ID:_1939_1994-1996_Kilifi_Kenya 1939_T4

value: ex-vivo culture, timepoint 4, 1939, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1915_1994-1996_Kilifi_Kenya 1915_T5

value: ex-vivo culture, timepoint 5, 1915, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_3180_1994-1996_Kilifi_Kenya 3180_T7

value: ex-vivo culture, timepoint 7, 3180, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1959_1994-1996_Kilifi_Kenya 1959_T2

value: ex-vivo culture, timepoint 2, 1959, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1959_1994-1996_Kilifi_Kenya 1959_T3

value: ex-vivo culture, timepoint 3, 1959, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1958_1994-1996_Kilifi_Kenya 1958_T1

value: ex-vivo culture, timepoint 1, 1958, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1980_1994-1996_Kilifi_Kenya 1980_T4

value: ex-vivo culture, timepoint 4, 1980, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1958_1994-1996_Kilifi_Kenya 1958_T0

value: ex-vivo culture, timepoint 0, 1958, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1939_1994-1996_Kilifi_Kenya 1939_T1

value: ex-vivo culture, timepoint 1, 1939, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1915_1994-1996_Kilifi_Kenya 1915_T3

value: ex-vivo culture, timepoint 3, 1915, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_Frozen10820_2010-2012_Kilifi_Kenya 10820_T5

value: ex-vivo culture, timepoint 5, Frozen10820, 2010-2012, Kilifi, Kenya, Low, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1958_1994-1996_Kilifi_Kenya 1958_T5

value: ex-vivo culture, timepoint 5, 1958, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1958_1994-1996_Kilifi_Kenya 1958_T7

value: ex-vivo culture, timepoint 7, 1958, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1958_1994-1996_Kilifi_Kenya 1958_T6

value: ex-vivo culture, timepoint 6, 1958, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1959_1994-1996_Kilifi_Kenya 1959_T1

value: ex-vivo culture, timepoint 1, 1959, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1920_1994-1996_Kilifi_Kenya 1920_T5

value: ex-vivo culture, timepoint 5, 1920, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1914_1994-1996_Kilifi_Kenya 1914_T2

value: ex-vivo culture, timepoint 2, 1914, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_4_patient_ID:_1920_1994-1996_Kilifi_Kenya 1920_T4

value: ex-vivo culture, timepoint 4, 1920, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1914_1994-1996_Kilifi_Kenya 1914_T1

value: ex-vivo culture, timepoint 1, 1914, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1920_1994-1996_Kilifi_Kenya 1920_T3

value: ex-vivo culture, timepoint 3, 1920, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1920_1994-1996_Kilifi_Kenya 1920_T2

value: ex-vivo culture, timepoint 2, 1920, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1920_1994-1996_Kilifi_Kenya 1920_T6

value: ex-vivo culture, timepoint 6, 1920, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1939_1994-1996_Kilifi_Kenya 1939_T0

value: ex-vivo culture, timepoint 0, 1939, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1958_1994-1996_Kilifi_Kenya 1958_T4

value: ex-vivo culture, timepoint 4, 1958, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1802_1994-1996_Kilifi_Kenya 1802_T5

value: ex-vivo culture, timepoint 5, 1802, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1802_1994-1996_Kilifi_Kenya 1802_T1

value: ex-vivo culture, timepoint 1, 1802, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1915_1994-1996_Kilifi_Kenya 1915_T0

value: ex-vivo culture, timepoint 0, 1915, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1802_1994-1996_Kilifi_Kenya 1802_T7

value: ex-vivo culture, timepoint 7, 1802, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1859_1994-1996_Kilifi_Kenya 1859_T3

value: ex-vivo culture, timepoint 3, 1859, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1915_1994-1996_Kilifi_Kenya 1915_T4

value: ex-vivo culture, timepoint 4, 1915, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1869_1994-1996_Kilifi_Kenya 1869_T6

value: ex-vivo culture, timepoint 6, 1869, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1914_1994-1996_Kilifi_Kenya 1914_T6

value: ex-vivo culture, timepoint 6, 1914, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1914_1994-1996_Kilifi_Kenya 1914_T4

value: ex-vivo culture, timepoint 4, 1914, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1869_1994-1996_Kilifi_Kenya 1869_T5

value: ex-vivo culture, timepoint 5, 1869, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_4_patient_ID:_1733_1994-1996_Kilifi_Kenya 1733_T4

value: ex-vivo culture, timepoint 4, 1733, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1869_1994-1996_Kilifi_Kenya 1869_T1

value: ex-vivo culture, timepoint 1, 1869, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1869_1994-1996_Kilifi_Kenya 1869_T2

value: ex-vivo culture, timepoint 2, 1869, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1915_1994-1996_Kilifi_Kenya 1915_T1

value: ex-vivo culture, timepoint 1, 1915, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1733_1994-1996_Kilifi_Kenya 1733_T3

value: ex-vivo culture, timepoint 3, 1733, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1802_1994-1996_Kilifi_Kenya 1802_T2

value: ex-vivo culture, timepoint 2, 1802, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1733_1994-1996_Kilifi_Kenya 1733_T1

value: ex-vivo culture, timepoint 1, 1733, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1802_1994-1996_Kilifi_Kenya 1802_T3

value: ex-vivo culture, timepoint 3, 1802, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1733_1994-1996_Kilifi_Kenya 1733_T0

value: ex-vivo culture, timepoint 0, 1733, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1914_1994-1996_Kilifi_Kenya 1914_T0

value: ex-vivo culture, timepoint 0, 1914, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1859_1994-1996_Kilifi_Kenya 1859_T0

value: ex-vivo culture, timepoint 0, 1859, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1802_1994-1996_Kilifi_Kenya 1802_T6

value: ex-vivo culture, timepoint 6, 1802, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1859_1994-1996_Kilifi_Kenya 1859_T2

value: ex-vivo culture, timepoint 2, 1859, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1859_1994-1996_Kilifi_Kenya 1859_T4

value: ex-vivo culture, timepoint 4, 1859, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1733_1994-1996_Kilifi_Kenya 1733_T6

value: ex-vivo culture, timepoint 6, 1733, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1733_1994-1996_Kilifi_Kenya 1733_T7

value: ex-vivo culture, timepoint 7, 1733, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1706_1994-1996_Kilifi_Kenya 1706_T4

value: ex-vivo culture, timepoint 4, 1706, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_5_patient_ID:_1706_1994-1996_Kilifi_Kenya 1706_T5

value: ex-vivo culture, timepoint 5, 1706, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1859_1994-1996_Kilifi_Kenya 1859_T5

value: ex-vivo culture, timepoint 5, 1859, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1869_1994-1996_Kilifi_Kenya 1869_T0

value: ex-vivo culture, timepoint 0, 1869, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1727_1994-1996_Kilifi_Kenya 1727_T2

value: ex-vivo culture, timepoint 2, 1727, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1802_1994-1996_Kilifi_Kenya 1802_T0

value: ex-vivo culture, timepoint 0, 1802, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1706_1994-1996_Kilifi_Kenya 1706_T1

value: ex-vivo culture, timepoint 1, 1706, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1727_1994-1996_Kilifi_Kenya 1727_T5

value: ex-vivo culture, timepoint 5, 1727, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1733_1994-1996_Kilifi_Kenya 1733_T2

value: ex-vivo culture, timepoint 2, 1733, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1706_1994-1996_Kilifi_Kenya 1706_T3

value: ex-vivo culture, timepoint 3, 1706, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1727_1994-1996_Kilifi_Kenya 1727_T4

value: ex-vivo culture, timepoint 4, 1727, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1690_1994-1996_Kilifi_Kenya 1690_T1

value: ex-vivo culture, timepoint 1, 1690, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1690_1994-1996_Kilifi_Kenya 1690_T3

value: ex-vivo culture, timepoint 3, 1690, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1727_1994-1996_Kilifi_Kenya 1727_T7

value: ex-vivo culture, timepoint 7, 1727, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1660_1994-1996_Kilifi_Kenya 1660_T2

value: ex-vivo culture, timepoint 2, 1660, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1690_1994-1996_Kilifi_Kenya 1690_T2

value: ex-vivo culture, timepoint 2, 1690, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1660_1994-1996_Kilifi_Kenya 1660_T1

value: ex-vivo culture, timepoint 1, 1660, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1660_1994-1996_Kilifi_Kenya 1660_T5

value: ex-vivo culture, timepoint 5, 1660, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_7_patient_ID:_1629_1994-1996_Kilifi_Kenya 1629_T7

value: ex-vivo culture, timepoint 7, 1629, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1629_1994-1996_Kilifi_Kenya 1629_T1

value: ex-vivo culture, timepoint 1, 1629, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1629_1994-1996_Kilifi_Kenya 1629_T3

value: ex-vivo culture, timepoint 3, 1629, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1624_1994-1996_Kilifi_Kenya 1624_T2

value: ex-vivo culture, timepoint 2, 1624, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1660_1994-1996_Kilifi_Kenya 1660_T4

value: ex-vivo culture, timepoint 4, 1660, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1706_1994-1996_Kilifi_Kenya 1706_T0

value: ex-vivo culture, timepoint 0, 1706, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1727_1994-1996_Kilifi_Kenya 1727_T1

value: ex-vivo culture, timepoint 1, 1727, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1690_1994-1996_Kilifi_Kenya 1690_T0

value: ex-vivo culture, timepoint 0, 1690, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1690_1994-1996_Kilifi_Kenya 1690_T6

value: ex-vivo culture, timepoint 6, 1690, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1660_1994-1996_Kilifi_Kenya 1660_T7

value: ex-vivo culture, timepoint 7, 1660, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1629_1994-1996_Kilifi_Kenya 1629_T5

value: ex-vivo culture, timepoint 5, 1629, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1706_1994-1996_Kilifi_Kenya 1706_T2

value: ex-vivo culture, timepoint 2, 1706, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1660_1994-1996_Kilifi_Kenya 1660_T3

value: ex-vivo culture, timepoint 3, 1660, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1623_1994-1996_Kilifi_Kenya 1623_T4

value: ex-vivo culture, timepoint 4, 1623, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1624_1994-1996_Kilifi_Kenya 1624_T7

value: ex-vivo culture, timepoint 7, 1624, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1727_1994-1996_Kilifi_Kenya 1727_T3

value: ex-vivo culture, timepoint 3, 1727, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1624_1994-1996_Kilifi_Kenya 1624_T1

value: ex-vivo culture, timepoint 1, 1624, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_3_patient_ID:_1623_1994-1996_Kilifi_Kenya 1623_T3

value: ex-vivo culture, timepoint 3, 1623, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1623_1994-1996_Kilifi_Kenya 1623_T6

value: ex-vivo culture, timepoint 6, 1623, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1590_1994-1996_Kilifi_Kenya 1590_T6

value: ex-vivo culture, timepoint 6, 1590, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1624_1994-1996_Kilifi_Kenya 1624_T6

value: ex-vivo culture, timepoint 6, 1624, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1623_1994-1996_Kilifi_Kenya 1623_T2

value: ex-vivo culture, timepoint 2, 1623, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1623_1994-1996_Kilifi_Kenya 1623_T0

value: ex-vivo culture, timepoint 0, 1623, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1624_1994-1996_Kilifi_Kenya 1624_T3

value: ex-vivo culture, timepoint 3, 1624, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1660_1994-1996_Kilifi_Kenya 1660_T0

value: ex-vivo culture, timepoint 0, 1660, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1624_1994-1996_Kilifi_Kenya 1624_T0

value: ex-vivo culture, timepoint 0, 1624, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1590_1994-1996_Kilifi_Kenya 1590_T1

value: ex-vivo culture, timepoint 1, 1590, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1590_1994-1996_Kilifi_Kenya 1590_T2

value: ex-vivo culture, timepoint 2, 1590, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1590_1994-1996_Kilifi_Kenya 1590_T3

value: ex-vivo culture, timepoint 3, 1590, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1590_1994-1996_Kilifi_Kenya 1590_T4

value: ex-vivo culture, timepoint 4, 1590, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1529_1994-1996_Kilifi_Kenya 1529_T3

value: ex-vivo culture, timepoint 3, 1529, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1529_1994-1996_Kilifi_Kenya 1529_T6

value: ex-vivo culture, timepoint 6, 1529, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1506_1994-1996_Kilifi_Kenya 1506_T7

value: ex-vivo culture, timepoint 7, 1506, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1624_1994-1996_Kilifi_Kenya 1624_T4

value: ex-vivo culture, timepoint 4, 1624, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_4_patient_ID:_1629_1994-1996_Kilifi_Kenya 1629_T4

value: ex-vivo culture, timepoint 4, 1629, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1590_1994-1996_Kilifi_Kenya 1590_T0

value: ex-vivo culture, timepoint 0, 1590, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1529_1994-1996_Kilifi_Kenya 1529_T1

value: ex-vivo culture, timepoint 1, 1529, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1529_1994-1996_Kilifi_Kenya 1529_T0

value: ex-vivo culture, timepoint 0, 1529, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1394_1994-1996_Kilifi_Kenya 1394_T7

value: ex-vivo culture, timepoint 7, 1394, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1506_1994-1996_Kilifi_Kenya 1506_T2

value: ex-vivo culture, timepoint 2, 1506, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1506_1994-1996_Kilifi_Kenya 1506_T4

value: ex-vivo culture, timepoint 4, 1506, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1394_1994-1996_Kilifi_Kenya 1394_T5

value: ex-vivo culture, timepoint 5, 1394, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1394_1994-1996_Kilifi_Kenya 1394_T4

value: ex-vivo culture, timepoint 4, 1394, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1506_1994-1996_Kilifi_Kenya 1506_T6

value: ex-vivo culture, timepoint 6, 1506, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1506_1994-1996_Kilifi_Kenya 1506_T1

value: ex-vivo culture, timepoint 1, 1506, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1394_1994-1996_Kilifi_Kenya 1394_T0

value: ex-vivo culture, timepoint 0, 1394, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1394_1994-1996_Kilifi_Kenya 1394_T6

value: ex-vivo culture, timepoint 6, 1394, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1387_1994-1996_Kilifi_Kenya 1387_T5

value: ex-vivo culture, timepoint 5, 1387, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1529_1994-1996_Kilifi_Kenya 1529_T2

value: ex-vivo culture, timepoint 2, 1529, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1387_1994-1996_Kilifi_Kenya 1387_T7

value: ex-vivo culture, timepoint 7, 1387, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1394_1994-1996_Kilifi_Kenya 1394_T1

value: ex-vivo culture, timepoint 1, 1394, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_3_patient_ID:_1387_1994-1996_Kilifi_Kenya 1387_T3

value: ex-vivo culture, timepoint 3, 1387, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1387_1994-1996_Kilifi_Kenya 1387_T4

value: ex-vivo culture, timepoint 4, 1387, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1387_1994-1996_Kilifi_Kenya 1387_T2

value: ex-vivo culture, timepoint 2, 1387, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1380_1994-1996_Kilifi_Kenya 1380_T7

value: ex-vivo culture, timepoint 7, 1380, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1394_1994-1996_Kilifi_Kenya 1394_T3

value: ex-vivo culture, timepoint 3, 1394, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1380_1994-1996_Kilifi_Kenya 1380_T4

value: ex-vivo culture, timepoint 4, 1380, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_0_patient_ID:_1387_1994-1996_Kilifi_Kenya 1387_T0

value: ex-vivo culture, timepoint 0, 1387, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1394_1994-1996_Kilifi_Kenya 1394_T2

value: ex-vivo culture, timepoint 2, 1394, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_7_patient_ID:_1354_1994-1996_Kilifi_Kenya 1354_T7

value: ex-vivo culture, timepoint 7, 1354, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1380_1994-1996_Kilifi_Kenya 1380_T3

value: ex-vivo culture, timepoint 3, 1380, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1380_1994-1996_Kilifi_Kenya 1380_T5

value: ex-vivo culture, timepoint 5, 1380, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1354_1994-1996_Kilifi_Kenya 1354_T4

value: ex-vivo culture, timepoint 4, 1354, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1354_1994-1996_Kilifi_Kenya 1354_T6

value: ex-vivo culture, timepoint 6, 1354, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_4_patient_ID:_1315_1994-1996_Kilifi_Kenya 1315_T4

value: ex-vivo culture, timepoint 4, 1315, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_1_patient_ID:_1387_1994-1996_Kilifi_Kenya 1387_T1

value: ex-vivo culture, timepoint 1, 1387, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_2_patient_ID:_1354_1994-1996_Kilifi_Kenya 1354_T2

value: ex-vivo culture, timepoint 2, 1354, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_6_patient_ID:_1315_1994-1996_Kilifi_Kenya 1315_T6

value: ex-vivo culture, timepoint 6, 1315, 1994-1996, Kilifi, Kenya, High, Expt C

value: strain P4, in vitro culture


title: ex-vivo_culture_timepoint_5_patient_ID:_1354_1994-1996_Kilifi_Kenya 1354_T5

value: ex-vivo culture, timepoint 5, 1354, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_5_patient_ID:_1315_1994-1996_Kilifi_Kenya 1315_T5

value: ex-vivo culture, timepoint 5, 1315, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1354_1994-1996_Kilifi_Kenya 1354_T3

value: ex-vivo culture, timepoint 3, 1354, 1994-1996, Kilifi, Kenya, High, Expt C


title: ex-vivo_culture_timepoint_3_patient_ID:_1315_1994-1996_Kilifi_Kenya 1315_T3

value: ex-vivo culture, timepoint 3, 1315, 1994-1996, Kilifi, Kenya, High, Expt C