title: BMSC Transwell Mono-culture - 24 hr - repeat 6

description: No additional information.

source_name: BMSC Transwell Mono-culture - 24 hr

treatment_protocol: In-vitro treatment: BMSCs from healthy donors were mono-cultured in a 1-um Transwell system (BD Biosciences, San Jose, CA USA). BMSC cells were harvested and RNA extracted.


title: genomic DNA from CD8+ NK cells Purified WBC subtype (NK8p2620)

status: Public on Feb 04 2014

type: genomic

city: Boston

first: William

middle: P

last: Accomando

state: MA

address: Kresge Bldg 911, 677 Huntington Ave

department: Epidemiology

country: USA

institute: Harvard School of Public Health

description:
NK8p2620
CD8+ NK cells Purified WBC subtype NK8p2620
Illumina VeraCode GGMA

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing:
Illumina GenomeStudio v2010.3
Unmethylated and methylated signal intensities are reported in a supplementary file on the Series record.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

growth_protocol: Not applicable

extract_protocol: Genomic DNA was extracted using QIAGEN Dneasy blood and tissue kit according to standard instructions

treatment_protocol: Leukocyte subtypes were purified via magnetic activated cell sorting (MACS) using kits from Miltenyi Biotec

tag: sample type

value: Purified WBC subtype

tag: disease state

value: normal

tag: sample subtype

value: CD8+ NK cells


title: BMSC Transwell Co-cultured with CD34 - 10 hr - repeat 3

type: RNA

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

description: No additional information.

hyb_protocol: Agilent Hybridization Protocol Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Agilent Scanning Protocol Other: Images of the arrays were acquired using a microarray scanner Scan G2505B and image analysis was performed using Scan Control software version 9.5 (Agilent Technologies). The images were extracted using the Feature Extraction Software (Agilent Technologies).

data_processing:
Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Agilent Technologies). Spot values were normalized using the default linear-lowess normalization. Partek Genomic Suite 6.4 (Partek Inc., St. Louis, MO, USA) and Ingenuity Pathway Analysis website (http://www.ingenuity.com, Ingenuity System Inc., Redwood City, CA, USA) were used for further data analysis.

molecule: total RNA

source_name: Universal Human Reference RNA

label_protocol:
Cy3 Labeling Protocol
Other: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit.

extract_protocol:
Strategene UHR RNA Extraction
Other: not available

tag: other

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

label_protocol:
Cy5 Labeling Protocol
Other: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit.

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was purified using miRNA Easy Kit (Qiagen). The RNA concentration was measured using a Nano Drop ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE, USA) and RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: In-vitro treatment: BMSCs from healthy donors were co-cultured with CD34+ cells isolated from G-CSF-mobilized peripheral blood stem cells from healthy donors. A 1-um Transwell system (BD Biosciences, San Jose, CA USA) was used to maintain the cultured BMSC and CD34+ cell populations separate from each other. BMSC cells were harvested and RNA extracted.

tag: tissue

value: Bone marrow

tag: cell type

value: Bone marrow derived stromal cells (BMSC)

value: Cells were harvested after 10 hours of co-culture.


title: Whole transcriptome analysis of INA6 cells using TileShuffle (permanently cultured in presence of IL-6 )

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells have been permanently cultured in IL-6. Intensities were processed with TileShuffle.

hyb_protocol: Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.

scan_protocol: Affymetrix Human Tiling 1.0 array were proceed using the GCS3000 7G system according to manufacturer's protocol.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. Intensities of perfect match (PM) probes were processed with TileShuffle (Otto C, Reiche K, Hackermüller J. "Detection of differentially expressed segments in tiling array data". Bioinformatics. 2012 Jun 1;28(11):1471-9. Epub 2012 Apr 6.) using a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, four GC content bins, 10000 permutations, and a q-value threshold of 0.05. In order to estimate the significance of a window score we repeatedly permute all probe intensities across the array while interchanging only those that belong to the same sequence-specific affinity bin, recompute the window scores, and compare them with the original ones. By counting the number of permuted windows with higher score, we estimate empirical p-values of windows, and report q-values adjusted according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995.).

label: biotin

source_name: Human multiple myeloma cells (INA6) permanently cultured in presence of IL-6

label_protocol: 10µg RNA were analyzed on Affymetrix Human Tiling 1.0 array set according to the manufacturer's protocol.

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

tag: cell line

tag: tumor

value: multiple myeloma

tag: treatment


title: CD34 Transwell Mono-culture - 10 hr - repeat 3

description: No additional information.

source_name: CD34 Transwell Mono-culture - 10 hr

treatment_protocol: In-vitro treatment: CD34+ cells isolated from G-CSF-mobilized peripheral blood stem cells from healthy donors were mono-cultured in a 1-um Transwell system (BD Biosciences, San Jose, CA USA). CD34+ cells were harvested and RNA extracted.

value: Blood

value: CD34+ cells

value: Cells were harvested after 10 hours of mono-culture.


title: genomic DNA from EDTA, o/n at room temp Human whole blood (3045EDTARt)

description:
3045EDTARt
EDTA, o/n at room temp Human whole blood 3045EDTARt
Illumina VeraCode GGMA

value: Human whole blood

value: EDTA, o/n at room temp


title: BMSC Transwell Mono-culture - 10 hr - repeat 6

description: No additional information.

source_name: BMSC Transwell Mono-culture - 10 hr


title: Whole transcriptome analysis of HFF cells using TileShuffle (G2 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G2 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G2 phase of mitotic cell cycle

value: HFF

tag: phase


title: CD34 Transwell Co-cultured with BMSC - 4 hr - repeat 3

description: No additional information.

treatment_protocol: In-vitro treatment: CD34+ cells isolated from G-CSF-mobilized peripheral blood stem cells from healthy donors were co-cultured with BMSCs from healthy donors. A 1-um Transwell system (BD Biosciences, San Jose, CA USA) was used to maintain the cultured BMSC and CD34+ cell populations separate from each other. CD34+ cells were harvested and RNA extracted.

value: Cells were harvested after 4 hours of co-culture.


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 withdrawal)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours

value: IL-6 has been withdrawn for 13 hours


title: Whole transcriptome analysis of HFF cells using TileShuffle (S phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in S phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in S phase of mitotic cell cycle

value: S


title: H1Xendo_ChIP_HeLa

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

description: H1X endogenous histone protein immunoprecipitated DNA

hyb_protocol: The labeled DNA was precipitated with 1 volume isopropanol. Hybridization mix including 15ug labeled DNA was prepared using Nimblegen hybridization kit (cat.#05583683001). Arrays were hybridized in Nimblegen hybridization system 4 station for 16-18 h at 42ºC, and then washed in 1XWash solution I, II and III (cat.#5584507001).Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/downloads/support/06584098001_NG_Epigenetics_UGuide_v1p0.pdf)

scan_protocol: Arrays were scanned on a Nimblegen MS200 scanner per manufacturer's protocol (http://www.nimblegen.com/downloads/support/scanner_ms200_manual_v1p0.pdf).

data_processing: Data were extracted and processed using DEVA software (http://www.nimblegen.com/downloads/support/06271090001_DEVA_UserGuide_v1p2.pdf)

source_name: H1X endogenous ChIP DNA from HeLa cells

label_protocol: 1 µg ChIP and input DNA was directly labeled by Klenow random priming with Cy5 and Cy3 nonamers  with Nimblegen Dual-color DNA labeling kit (cat.# 06370250001) following manufacturer's user's guide Chip-chip arrays v6.2

growth_protocol: DMEM GlutaMax medium + 10%FBS, 1%penicillin/streptomycin

extract_protocol: T47D-MTVL or HeLa cells cells were fixed using 1% formaldehyde, harvested and sonicated using a Diagenode Bioruptor to generate chromatin fragments between 200 and 500 bp. To perform the chromatin immunoprecipitation, 30 µg of chromatin was immunoprecipitated overnight using the indicated antibody. Rabbit IgG (Santa Cruz Biothechnology) was used as a control for nonspecific interaction of DNA. Input was prepared with 10% of the chromatin material used for an immunoprecipitation. Immunocomplexes were recovered using Protein A magnetic beads from Millipore. Beads with bound antibody/protein/DNA complexes were washed, decross-linked at 65ºC overnight and immunoprecipitated DNA was recovered using the IPure Kit from Diagenode.

value: HeLa

tag: gender

value: female

value: cervical cancer

tag: antibody

value: anti-H1X (Abcam 31972)

source_name: INPUT DNA from HeLa cells


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G1 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle


title: CD34 Transwell Mono-culture - 4 hr - repeat 3

description: No additional information.

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: CD34 Transwell Mono-culture - 4 hr

value: Cells were harvested after 4 hours of mono-culture.


title: genomic DNA from B-cells Purified WBC subtype (B1869)

description:
B1869
B-cells Purified WBC subtype B1869
Illumina VeraCode GGMA

source_name: B-cells Purified WBC subtype B1869

value: Purified WBC subtype

value: normal

value: B-cells


title: BMSC Transwell Co-cultured with CD34 - 4 hr - repeat 3

description: No additional information.

value: Bone marrow

value: Bone marrow derived stromal cells (BMSC)


title: genomic DNA from Citrate, o/n at 4C Human whole blood (3045Cit4C)

description:
3045Cit4C
Citrate, o/n at 4C Human whole blood 3045Cit4C
Illumina VeraCode GGMA

value: Human whole blood

value: Citrate, o/n at 4C


title: CD34 Transwell Mono-culture - 24 hr - repeat 2

description: No additional information.

source_name: CD34 Transwell Mono-culture - 24 hr

value: Blood

value: CD34+ cells

value: Cells were harvested after 24 hours of mono-culture.


title: genomic DNA from Monocytes Purified WBC subtype (Mono1972)

description:
Mono1972
Monocytes Purified WBC subtype Mono1972
Illumina VeraCode GGMA

source_name: Monocytes Purified WBC subtype Mono1972

value: Monocytes


title: BMSC Transwell Mono-culture - 4 hr - repeat 6

description: No additional information.

source_name: BMSC Transwell Mono-culture - 4 hr


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle

value: HFF


title: P53_ind_chipF_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set after induction of P53 expression. Intensities were processed with TileShuffle.

source_name: Colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53

value: colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 restimulation)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours

value: multiple myeloma


title: H3_ChIP_T47D-MTVL

description: H3 endogenous histone protein immunoprecipitated DNA

source_name: H3 ChIP DNA from T47D-MTVL breast cancer cells

growth_protocol: RPMI 1640 medium + 10%FBS, 1%glutamine, 1%penicillin/streptomycin

value: female

value: breast cancer ductal carcinoma

value: anti-H3 (Abcam 1791)

source_name: INPUT DNA from T47D-MTVL cells


title: Whole transcriptome analysis of INA6 cells using TileShuffle (permanently cultured in presence of IL-6 )

source_name: Human multiple myeloma cells (INA6) permanently cultured in presence of IL-6


title: genomic DNA from EDTA, o/n at room temp Human whole blood (3082EDTARt)

description:
3082EDTARt
EDTA, o/n at room temp Human whole blood 3082EDTARt
Illumina VeraCode GGMA

value: EDTA, o/n at room temp


value: restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


value: IL-6 has been withdrawn for 13 hours


title: H1Xendo_ChIP_T47D-MTVL

source_name: H1X endogenous ChIP DNA from T47D-MTVL breast cancer cells

value: anti-H1X (Abcam 31972)


title: H1.4-HA_ChIP_T47D-MTVL

description: H1.4-HA histone protein immunoprecipitated DNA

source_name: H1.4-HA ChIP DNA from H1.4-HA stably overexpressing T47D-MTVL breast cancer cells

tag: stably overexpressing

source_name: INPUT DNA from H1.4-HA stably overexpressing T47D-MTVL cells


title: H1.2-HA_ChIP_T47D-MTVL

description: H1.2-HA histone protein immunoprecipitated DNA

source_name: H1.2-HA ChIP DNA from H1.2-HA stably overexpressing T47D-MTVL breast cancer cells

value: anti-H1.2 (Abcam 4086)

source_name: INPUT DNA from H1.2-HA stably overexpressing T47D-MTVL cells


title: P53_nor_chipF_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set. Intensities were processed with TileShuffle.

source_name: Colorectal carcinoma cells with defunct P53 (D53wt cells)

value: colorectal carcinoma cells with defunct P53 (D53wt cells)


source_name: Human foreskin fibroblasts (HFF) in G2 phase of mitotic cell cycle


title: genomic DNA from CD16+ NK cells Purified WBC subtype (NK16p2288)

description:
NK16p2288
CD16+ NK cells Purified WBC subtype NK16p2288
Illumina VeraCode GGMA

value: Purified WBC subtype

value: normal

value: CD16+ NK cells


source_name: Human foreskin fibroblasts (HFF) in S phase of mitotic cell cycle

value: S


title: H1.2endo_ChIP_HeLa

description: H1.2 endogenous histone protein immunoprecipitated DNA

source_name: H1.2 endogenous ChIP DNA from HeLa cells

value: HeLa

value: cervical cancer

source_name: INPUT DNA from HeLa cells


source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle

value: HFF


title: H1.2endo_ChIP_T47D-MTVL

source_name: H1.2 endogenous ChIP DNA from T47D-MTVL breast cancer cells


title: genomic DNA from CD4+ T-cells Purified WBC subtype (Th1702)

description:
Th1702
CD4+ T-cells Purified WBC subtype Th1702
Illumina VeraCode GGMA

value: CD4+ T-cells


description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells have been permanently cultured in IL-6. Intensities were processed with TileShuffle.

value: multiple myeloma

value: permanently cultured in presence of IL-6


title: genomic DNA from CD8+ T-cells Purified WBC subtype (Tc2615)

description:
Tc2615
CD8+ T-cells Purified WBC subtype Tc2615
Illumina VeraCode GGMA

value: CD8+ T-cells


title: CD34 Transwell Co-cultured with BMSC - 24 hr - repeat 2

description: No additional information.

source_name: Universal Human Reference RNA

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

value: Blood

value: CD34+ cells

value: Cells were harvested after 24 hours of co-culture.


title: H1.0-HA_ChIP_T47D-MTVL

description: H1.0-HA histone protein immunoprecipitated DNA

source_name: H1.0-HA ChIP DNA from H1.0-HA stably overexpressing T47D-MTVL breast cancer cells

value: female

value: breast cancer ductal carcinoma

value: anti-HA (Abcam 9110)

source_name: INPUT DNA from H1.0-HA stably overexpressing T47D-MTVL cells


title: P53_ind_chipM_TileShuffle

source_name: Colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53

value: colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53


title: genomic DNA from EDTA, Fresh Human whole blood (3159EDTAFr)

description:
3159EDTAFr
EDTA, Fresh Human whole blood 3159EDTAFr
Illumina VeraCode GGMA

value: Human whole blood

value: normal

value: EDTA, Fresh


title: BMSC Transwell Co-cultured with CD34 - 24 hr - repeat 2

description: No additional information.

value: Bone marrow

value: Bone marrow derived stromal cells (BMSC)


source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle

value: HFF


title: P53_nor_chipM_TileShuffle

value: colorectal carcinoma cells with defunct P53 (D53wt cells)


title: H1.3-HA_ChIP_T47D-MTVL

description: H1.3-HA histone protein immunoprecipitated DNA

source_name: H1.3-HA ChIP DNA from H1.3-HA stably overexpressing T47D-MTVL breast cancer cells

source_name: INPUT DNA from H1.3-HA stably overexpressing T47D-MTVL cells


title: P53_nor_chipD_TileShuffle


title: CD34 Transwell Co-cultured with BMSC - 10 hr - repeat 2

description: No additional information.

value: Cells were harvested after 10 hours of co-culture.


title: BMSC Transwell Co-cultured with CD34 - 10 hr - repeat 2

description: No additional information.


title: CD34 Transwell Mono-culture - 10 hr - repeat 2

description: No additional information.

source_name: CD34 Transwell Mono-culture - 10 hr

value: Cells were harvested after 10 hours of mono-culture.


title: BMSC Transwell Mono-culture - 24 hr - repeat 5

description: No additional information.

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: BMSC Transwell Mono-culture - 24 hr

value: Cells were harvested after 24 hours of mono-culture.


source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours

value: multiple myeloma


title: genomic DNA from Pan-T cells Purified WBC subtype (Tpan1754)

description:
Tpan1754
Pan-T cells Purified WBC subtype Tpan1754
Illumina VeraCode GGMA

value: Purified WBC subtype

value: Pan-T cells


title: P53_ind_chipD_TileShuffle


title: genomic DNA from EDTA, Fresh Human whole blood (3045EDTAFr)

description:
3045EDTAFr
EDTA, Fresh Human whole blood 3045EDTAFr
Illumina VeraCode GGMA


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 withdrawal)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours

value: IL-6 has been withdrawn for 13 hours


title: CD34 Transwell Co-cultured with BMSC - 24 hr - repeat 1

description: No additional information.

value: Blood

value: CD34+ cells

value: Cells were harvested after 24 hours of co-culture.


title: CD34 Transwell Co-cultured with BMSC - 4 hr - repeat 2

description: No additional information.

value: Cells were harvested after 4 hours of co-culture.


title: genomic DNA from CD8- NK cells Purified WBC subtype (NK8m2626)

description:
NK8m2626
CD8- NK cells Purified WBC subtype NK8m2626
Illumina VeraCode GGMA

value: normal

value: CD8- NK cells


title: H1.5-HA_ChIP_T47D-MTVL

description: H1.5-HA histone protein immunoprecipitated DNA

source_name: H1.5-HA ChIP DNA from H1.5-HA stably overexpressing T47D-MTVL breast cancer cells

value: female

value: breast cancer ductal carcinoma

source_name: INPUT DNA from H1.5-HA stably overexpressing T47D-MTVL cells


title: genomic DNA from Pan-NK cells Purified WBC subtype (NKpan1879)

description:
NKpan1879
Pan-NK cells Purified WBC subtype NKpan1879
Illumina VeraCode GGMA

value: Pan-NK cells


title: genomic DNA from Granulocytes Purified WBC subtype (Gran532)

description:
Gran532
Granulocytes Purified WBC subtype Gran532
Illumina VeraCode GGMA

value: Granulocytes


title: genomic DNA from Citrate, o/n at 4C Human whole blood (3082Cit4C)

description:
3082Cit4C
Citrate, o/n at 4C Human whole blood 3082Cit4C
Illumina VeraCode GGMA

value: Human whole blood

value: Citrate, o/n at 4C


title: CD34 Transwell Mono-culture - 4 hr - repeat 2

description: No additional information.

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: CD34 Transwell Mono-culture - 4 hr

value: Cells were harvested after 4 hours of mono-culture.


title: genomic DNA from Citrate, o/n at 4C Human whole blood (3021Cit4C)

description:
3021Cit4C
Citrate, o/n at 4C Human whole blood 3021Cit4C
Illumina VeraCode GGMA


title: genomic DNA from Heparin, Fresh Human whole blood (3093HepFr)

description:
3093HepFr
Heparin, Fresh Human whole blood 3093HepFr
Illumina VeraCode GGMA

value: Heparin, Fresh


title: platelet with TPO

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

country: China

institute: Nanjing University

description:
platelet with TPO
microRNA profiling

data_processing: Data were analyzed using RQ Manager Software version 1.2 and 7900 Sequence Detection System 2.4 (Applied Biosystems). For the normalization it uses U6 snRNA as endogenous control miRNA.

label: FAM

source_name: blood

label_protocol: Standard Applied Biosystems protocol.

growth_protocol: Platelet-rich plasma was diluted in washing buffer, and the pure platelets were  isolated by centrifuged .

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: Platelets were recovered in suspension buffer at the concentration of 4–5×108 platelets/ml. Aliquots of the platelet suspensions were activated in the presence of 2.5 mM CaCl2 with 0ng/ml or 1 ng/ml TPO,

value: platelet

value: TPO


title: BMSC Transwell Co-cultured with CD34 - 24 hr - repeat 1

description: No additional information.

value: Bone marrow

value: Bone marrow derived stromal cells (BMSC)


title: BMSC Transwell Co-cultured with CD34 - 4 hr - repeat 2

description: No additional information.


title: PAXgene whole blood, Control, Day_5, ID=17

city: Kingswood

first: Grant

last: Parnell

state: NSW

address: Nepean Hospital

department: Nepean Clinical School

country: Australia

institute: University of Sydney

description:
4950679036_J
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

hyb_protocol: Hybridization protocol as per the Illumina Whole-Genome Gene Expression Direct Hybridization Experienced User Guide.

scan_protocol: Scanned using default parameters on Illumina BeadArray Reader.

data_processing: Data pre-processed in GenomeStudio. A detection p value of <0.005 was required in at least 1 sample for probe to be retained. Probes which passed this filter were uploaded into BRB-ArrayTools.

source_name: PAXgene whole blood, Control, Day 5, ID=17

label_protocol: cRNA prepared using Ambion Illumina TotalPrep RNA Amplification Kit.

extract_protocol: RNA was extracted using PAXgene blood RNA kit v2 (PreAnalytix).

value: whole blood

tag: disease status

value: healthy

value: F

tag: age (years)

tag: severity (apacheii)

tag: neutrophil proportion

tag: site of infection


title: PAXgene whole blood, Control, Day_5, ID=12

description:
4950679034_L
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=12


title: CD34 Transwell Mono-culture - 24 hr - repeat 1

description: No additional information.

source_name: Universal Human Reference RNA

source_name: CD34 Transwell Mono-culture - 24 hr

value: Blood

value: CD34+ cells

value: Cells were harvested after 24 hours of mono-culture.


title: PAXgene whole blood, Control, Day_5, ID=16

description:
4950679036_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=16


title: PAXgene whole blood, Control, Day_5, ID=18

description:
4950679036_L
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=18

value: M


title: platelet without TPO

description:
platelet without TPO
microRNA profiling

value: control


title: CD34 Transwell Co-cultured with BMSC - 10 hr - repeat 1

description: No additional information.

value: Cells were harvested after 10 hours of co-culture.


title: BMSC Transwell Mono-culture - 24 hr - repeat 4

description: No additional information.


title: BMSC Transwell Mono-culture - 10 hr - repeat 5

description: No additional information.

source_name: BMSC Transwell Mono-culture - 10 hr

value: Cells were harvested after 10 hours of mono-culture.


title: BMSC Transwell Mono-culture - 4 hr - repeat 5

description: No additional information.

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

source_name: BMSC Transwell Mono-culture - 4 hr


title: CD34 Transwell Mono-culture - 10 hr - repeat 1

description: No additional information.


title: PAXgene whole blood, Control, Day_5, ID=11

description:
4950679034_J
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=11


title: PAXgene whole blood, Control, Day_5, ID=10

description:
4950679034_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=10


title: PAXgene whole blood, Control, Day_5, ID=15

description:
4950679036_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=15


title: PAXgene whole blood, Control, Day_5, ID=9

description:
4950679034_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=9


title: PAXgene whole blood, Control, Day_5, ID=14

description:
4950679036_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=14


title: B_WT_1_2_48h

city: ATHENS

first: Scott

middle: E

last: Gold

state: GA

address: 950 COLLEGE STATION RD

department: Toxicology and Mycotoxin Research

institute: USDA ARS

hyb_protocol: Arrays were hybridized using standardized Nimblegen protocol (please see http://www.nimblegen.com/index.html)

scan_protocol: Arrays were scanned using standardized Nimblegen protocol (please see http://www.nimblegen.com/index.html)

data_processing:
Data Processing was performed using Standardized Nimblegen protocol (please see http://www.nimblegen.com/index.html)
signal calculated by Nimblegen software. The values in the matrix table are expression avarages of 14 probes per gene per block. There were four blocks on 1-plex Nimblegen chip.

organism: Mycosarcoma maydis

source_name: RNA from wild type (WT) fungal cells 48h in culture

label_protocol: Samles were labeled using standardized Nimblegen protocol (please see http://www.nimblegen.com/index.html)

growth_protocol: 48 hour in culture media

extract_protocol: Wild-type and ∆ust1 strains were grown in potato dextrose broth (PDB) for 48 h at 30oC. To allow effective comparison with other array data generated by U. maydis researchers, cells were then transferred to liquid array medium (6.25% Holiday salt solution, 30mM L-glutamine, 1% glucose, pH7.0, filter sterilized) at 30 C. Total RNA samples from WT 1/2  and ∆ust1 mutant strains grown in array medium for 24 h (mutant’s filamentous phase), and 48 h (mutant’s spore-like structure formation phase) were extracted and purified (Sigma Spectrum Plant Total RNA Kit, Cat.No.STRN50).

treatment_protocol: 30 C shaker (250 rpm)

tag: genotype/variation

tag: culture time

value: 48 hour


title: B_ust1_14_25_24h

source_name: RNA from mutant (ust1) fungal cells 24h in culture

growth_protocol: 24 hour in culture media

value: ust1 mutant (14/25)

value: 24 hour


title: B_WT_1_2_24h

source_name: RNA from wild type (WT) fungal cells 24h in culture


title: A_ust1_14_25_48h

source_name: RNA from mutant (ust1) fungal cells 48h in culture


title: PAXgene whole blood, Control, Day_5, ID=8

description:
4950679034_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=8


title: PAXgene whole blood, Control, Day_5, ID=6

description:
4950679008_L
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=6


title: CD34 Transwell Co-cultured with BMSC - 4 hr - repeat 1

description: No additional information.

source_name: Universal Human Reference RNA

tag: other

value: Cells were harvested after 4 hours of co-culture.


title: PAXgene whole blood, Control, Day_5, ID=5

description:
4950679008_J
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=5

tag: tissue


title: BMSC Transwell Co-cultured with CD34 - 10 hr - repeat 1

description: No additional information.

value: Bone marrow

tag: cell type


title: A_ust1_14_25_24h


title: B_ust1_14_25_48h


title: PAXgene whole blood, Control, Day_5, ID=1

description:
4950679008_B
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=1


title: BMSC Transwell Mono-culture - 10 hr - repeat 4

description: No additional information.

value: Bone marrow derived stromal cells (BMSC)


title: CD34 Transwell Mono-culture - 4 hr - repeat 1

description: No additional information.

source_name: CD34 Transwell Mono-culture - 4 hr

value: Cells were harvested after 4 hours of mono-culture.


title: PAXgene whole blood, Control, Day_5, ID=7

description:
4950679034_B
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=7

value: whole blood

value: healthy


title: PAXgene whole blood, Control, Day_5, ID=4

description:
4950679008_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=4


title: PAXgene whole blood, Control, Day_5, ID=3

description:
4950679008_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=3


title: PAXgene whole blood, sepsis_survivor, Day_5, ID=54

description:
5445295021_K
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 5, ID=54

value: sepsis survivor

value: lung


title: PAXgene whole blood, sepsis_survivor, Day_5, ID=46

description:
5447354026_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 5, ID=46

value: F


title: PAXgene whole blood, Control, Day_5, ID=2

description:
4950679008_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=2


title: A_WT_1_2_48h


title: PAXgene whole blood, sepsis_survivor, Day_5, ID=50

description:
5447354026_L
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 5, ID=50

value: Other


title: TF-1alpha + BMSCs from Separate Mono-culture - 24 hr

description: No additional information.

treatment_protocol: In-vitro treatment: AML cell line, TF-1alpha, cells and BMSCs from healthy donors were cultured as separate monocultures. The cells from both populations were harvested and pooled together and RNA extracted.

tag: cell line

value: CD34+/CD38- myeloid leukemia cells (TF-1alpha) and Bone marrow derived stromal cells (BMSCs)

tag: disease state

value: myeloid leukemia

value: Cells were harvested after 24 hours of mono-culture.


title: PAXgene whole blood, sepsis_survivor, Day_5, ID=51

description:
5447354040_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 5, ID=51

value: M


title: PAXgene whole blood, sepsis_survivor, Day_5, ID=35

description:
4674281014_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 5, ID=35


title: BMSC Transwell Co-cultured with CD34 - 4 hr - repeat 1

description: No additional information.

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.


title: Human oral microbiome from patients with advanced periodontitis PH24

city: Norman

first: Qichao

last: Tu

state: OK

address: 101 David L Boren Blvd

institute: University of Oklahoma

hyb_protocol: DNA was suspended in hybridization buffer and then kept at 65°C until hybridization. Hybridizations were performed at 42°C for 10 h using a Tecan HS4800 Pro hybridization station

scan_protocol: Arrays were scanned with a ScanArray 500 microarray scanner  at 633 nm using a laser power of 90% and a photomultiplier tube (PMT) gain of 75%.

data_processing: Signal intensity were normalized by CORS universal standard probes (Liang et. al 2010 AEM), probes with SNR<2 are removed, normalized signal intensities was calculated for further statistical analysis. We used minimal signal intensity of 1000 and SNR (Signal to Noise Ratio) cutoff of 2 for positive callings of the presence of a gene.

organism: human metagenome

label_protocol: DNA was labeled with the fluorescent dye Cy5 (GE Healthcare) by random priming

extract_protocol: For oral microbiome sampling, bacteria were separated from the paper-points by vortexing. The paper points were discarded and community DNA was extracted using the QIAamp TM DNA micro Kit (QIAGEN Sciences, Maryland, USA) following the manufacturer’s instructions and adding a lysozyme (3 mg/mL, 1.5 h) treatment step. For gut microbiome sampling, all fecal samples were immediately frozen on collection and stored at -70℃ before analysis. A frozen aliquot (200 mg) of each fecal sample was added to a 2.0-ml screwcap vial containing 300 mg glass beads of 0.1 mm diameter (Sigma, St. Louis, MO, USA), and kept on ice until the addition of 1.4-ml ASL buffer from the QIAamp DNA Stool Mini Kit (Qiagen, Valencia, CA, USA). Samples were immediately subjected to beadbeating (45 s, speed 6.5) using a FastPrep machine (Bio 101, Morgan Irvine, CA, USA), prior to the initial incubation for heat and chemical lysis at 95 ℃ for 5 minutes. Subsequent steps of DNA extraction followed the QIAamp kit protocol for pathogen detection.

tag: source


title: BMSC Transwell Mono-culture - 4 hr - repeat 4

description: No additional information.

source_name: BMSC Transwell Mono-culture - 4 hr


title: PAXgene whole blood, sepsis_survivor, Day_5, ID=49

description:
5447354008_J
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 5, ID=49


title: Human oral microbiome from patients with advanced periodontitis PH22


title: A_WT_1_2_24h

source_name: RNA from wild type (WT) fungal cells 24h in culture


title: PAXgene whole blood, sepsis_survivor, Day_5, ID=30

description:
4674281008_L
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 5, ID=30

value: blood


title: PAXgene whole blood, sepsis_survivor, Day_5, ID=45

description:
5447354008_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 5, ID=45


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=50

description:
5447354026_K
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=50


title: PAXgene whole blood, sepsis_survivor, Day_5, ID=43

description:
5445295025_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 5, ID=43


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=48

description:
5447354026_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=48


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=51

description:
5447354040_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=51


title: PAXgene whole blood, sepsis_survivor, Day_5, ID=42

description:
5445295027_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 5, ID=42


title: TF-1alpha Transwell Mono-culture - 24 hr

description: No additional information.

treatment_protocol: In-vitro treatment: AML cell line, TF-1alpha, cells were mono-cultured in a 1-um Transwell system (BD Biosciences, San Jose, CA USA). TF-1alpha cells were harvested and RNA extracted.

value: CD34+/CD38- myeloid leukemia cells

source_name: Universal Human Reference RNA


title: TF-1alpha + BMSCs in Direct Co-culture - 24 hr

description: No additional information.

treatment_protocol: In-vitro treatment: AML cell line, TF-1alpha, cells were co-cultured with BMSCs from healthy donors. The two populations were cultured together in direct contact in the same well without any membrane separation. The cells from both populations were harvested together and RNA extracted.

value: Cells were harvested after 24 hours of co-culture.


title: PAXgene whole blood, sepsis_survivor, Day_5, ID=33

description:
4674281014_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 5, ID=33


title: TF-1alpha Transwell Co-cultured with BMSCs - 24 hr

description: No additional information.

treatment_protocol: In-vitro treatment: AML cell line, TF-1alpha, cells were co-cultured with BMSCs from healthy donors. A 1-um Transwell system (BD Biosciences, San Jose, CA USA) was used to maintain the cultured BMSC and TF-1alpha cell populations separate from each other. TF-1alpha cells were harvested and RNA extracted.

value: Bone marrow


title: TF-1alpha + BMSCs from Separate Mono-culture - 10 hr

description: No additional information.

value: Cells were harvested after 10 hours of mono-culture.


title: BMSC Transwell Mono-culture - 24 hr - repeat 3

description: No additional information.

source_name: BMSC Transwell Mono-culture - 24 hr

value: Bone marrow derived stromal cells (BMSC)


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=54

description:
5445295021_J
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=54

value: whole blood


title: BMSC Transwell Co-cultured with TF-1alpha - 24 hr

description: No additional information.

treatment_protocol: In-vitro treatment: BMSCs from healthy donors were co-cultured with AML cell line, TF-1alpha, with phenotype CD34+/CD38-. A 1-um Transwell system (BD Biosciences, San Jose, CA USA) was used to maintain the cultured BMSC and TF-1alpha cell populations separate from each other. BMSC cells were harvested and RNA extracted.


title: Human oral microbiome from patients with advanced periodontitis PH19


title: Human oral microbiome from patients with advanced periodontitis PH21


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=49

description:
5447354008_I
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=49


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=35

description:
4674281014_I
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=35


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=45

description:
5447354008_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=45


title: PAXgene whole blood, Control, Day_5, ID=13

description:
4950679036_B
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 5, ID=13

value: healthy


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=43

description:
5445295025_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=43

value: sepsis survivor


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=46

description:
5447354026_B
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=46

value: lung


title: Human oral microbiome from patients with advanced periodontitis PH8


title: Human oral microbiome from patients with advanced periodontitis PH9


title: TF-1alpha + BMSCs in Direct Co-culture - 10 hr

description: No additional information.

value: Cells were harvested after 10 hours of co-culture.


title: TF-1alpha Transwell Mono-culture - 10 hr

description: No additional information.


title: Human oral microbiome from patients with advanced periodontitis PH11


title: Human oral microbiome from patients with advanced periodontitis PH12


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=41

description:
5125398047_J
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=41

value: F


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=53

description:
5447354040_K
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=53

value: Other


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=39

description:
5125398047_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=39


title: BMSC Transwell Mono-culture - 10 hr - repeat 3

description: No additional information.

source_name: BMSC Transwell Mono-culture - 10 hr


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=42

description:
5445295027_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=42


title: TF-1alpha Transwell Co-cultured with BMSCs - 10 hr

description: No additional information.

value: myeloid leukemia


title: Human oral microbiome from patients with advanced periodontitis PH5


title: Human oral microbiome from patients with advanced periodontitis PH6


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=30

description:
4674281009_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=30


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=52

description:
5447354040_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=52


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=54

description:
5125398041_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=54


title: BMSC Transwell Co-cultured with TF-1alpha - 10 hr

description: No additional information.

source_name: Universal Human Reference RNA


title: PAXgene whole blood, sepsis_survivor, Day_4, ID=33

description:
4674281014_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 4, ID=33


title: Human oral microbiome from patients with advanced periodontitis PH7


title: Human oral microbiome from patients with advanced periodontitis PH3


title: TF-1alpha Transwell Mono-culture - 4 hr

description: No additional information.

source_name: TF-1alpha Transwell Mono-culture - 4 hr

value: Cells were harvested after 4 hours of mono-culture.


title: TF-1alpha + BMSCs from Separate Mono-culture - 4 hr

description: No additional information.

value: CD34+/CD38- myeloid leukemia cells (TF-1alpha) and Bone marrow derived stromal cells (BMSCs)


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=50

description:
5447354026_J
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=50


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=49

description:
5447354008_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=49


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=51

description:
5447354040_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=51

value: M


title: TF-1alpha Transwell Co-cultured with BMSCs - 4 hr

description: No additional information.

value: Cells were harvested after 4 hours of co-culture.

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.


title: Human oral microbiome from patients with moderate periodontitis PL16


title: TF-1alpha + BMSCs in Direct Co-culture - 4 hr

description: No additional information.


title: doxorubicin_6 hours_rep2 (exon-level)

city: ORSAY

first: Martin

last: Dutertre

address: Rue Henri Becquerel

country: France

institute: INSERM

description:
MCF17 treated by doxorubicin for 6 hours
MCF7_DOXO_n2

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200ul of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Analyses were obtained using the Affymetrix Power Tools software ; core probesets, and antigenomic probes for background correction. The plier-gcbg-sketch algorithm was used to determine gene-level expression data and the RMA-sketch algorithm for the exon-level expression data.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.ps (for exon-level analyses)

source_name: MCF7 cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: MCF7 cells were maintained in DMEM with 10% fetal bovine serum in a CO2 humidified chamber at 37 °C

extract_protocol: Total RNA was isolated using Trizol total RNA isolation reagent (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: Cells were treated with doxorubicin (2 µg/ml) or 0.1% DMSO as a control.

tag: tumor stage

value: ER+ breast cancer cell line

tag: agent

value: doxorubicin


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=47

description:
5445295025_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=47

tag: gender


title: Human oral microbiome from patients with advanced periodontitis PH1


title: Human oral microbiome from patients with moderate periodontitis PL17


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=48

description:
5447354026_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=48


title: Human oral microbiome from patients with moderate periodontitis PL15


title: doxorubicin_6 hours_rep3 (exon-level)

description:
MCF17 treated by doxorubicin for 6 hours
MCF7_DOXO_n3


title: T84_1h_ST_Rep2

city: Bangalore

first: Sandhya

middle: S

last: Visweswariah

state: Karnataka

address: GA-09, Dept of MRDG, Biological Sciences Building, Indian Institute of Science

department: Molecular Reproduction, Development and Genetics

country: India

institute: Indian Institute of Science

hyb_protocol: 825 ng of labelled cRNA each from clones and vector control were mixed with blocking agent and fragmentation buffer followed by incubation at 65 °C for 30 min. This is followed by addition of 55 ul of 2x GEx Hybridization Buffer HI-RPM to stop the fragmentation reaction. 100 ul of the reaction added to each array.

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization.

source_name: T84 control

label_protocol: 200 ng of RNA each from control and 1 h ST treated cells was used. Labeling of the RNA was done using the Low RNA Input Linear Amplification Kit (Agilent Technologies, USA). Briefly, 200 ng of RNA was reverse transcribed using T7 promoter attached Oligo-dT primers at 40 °C for 2 h followed by 65 °C for 15 min. This cDNA was transcribed using T7 polymerase with respective labelled nucleotides at 40 °C for 2 h. Labelled cRNA was purified using RNeasy mini column.

growth_protocol: T84 cells  were maintained in DMEM-F12 (Sigma-Aldrich, USA) supplemented with 5% fetal bovine serum (Invitrogen corporation, USA), 50 units/mL penicillin and 50 µg/mL streptomycin (Sigma-Aldrich, USA) at 37 °C in a humidified chamber with 5% CO2.

extract_protocol: Total RNA extracted using RNeasy Mini Kit (Qiagen, USA) according to manufacturer's instructions

value: T84 colorectal carcinoma cell line

source_name: T84 1h ST

treatment_protocol: T84 cells were treated with 100 nM ST for 1 h at 37 °C


title: Human oral microbiome from patients with moderate periodontitis PL14


title: control_6 hours_rep2 (exon-level)

description:
MCF17 treated by DMSO for 6 hours
MCF7_CTRL_n2

value: control


title: Human oral microbiome from patients with moderate periodontitis PL11


title: BMSC Transwell Mono-culture - 4 hr - repeat 3

description: No additional information.

source_name: BMSC Transwell Mono-culture - 4 hr

value: Bone marrow

value: Bone marrow derived stromal cells (BMSC)


title: K562 + BMSCs in Direct Co-culture - 24 hr

description: No additional information.

treatment_protocol: In-vitro treatment: CD34- chronic myeloid leukemia cell line, K562, cells were co-cultured with BMSCs from healthy donors. The two populations were cultured together in direct contact in the same well without any membrane separation. The cells from both populations were harvested together and RNA extracted.

value: CD34- myeloid leukemia cells (K562) and Bone marrow derived stromal cells (BMSC)

value: Cells were harvested after 24 hours of co-culture.


title: doxorubicin_6 hours_rep1 (exon-level)

description:
MCF17 treated by doxorubicin for 6 hours
MCF7_DOXO_n1


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=45

description:
5447354008_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=45

value: whole blood

value: sepsis survivor

value: blood


title: K562 + BMSCs from Separate Mono-culture - 24 hr

description: No additional information.

treatment_protocol: In-vitro treatment: CD34- chronic myeloid leukemia cell line, K562, cells and BMSCs from healthy donors were cultured as separate monocultures. The cells from both populations were harvested and pooled together and RNA extracted.

value: myeloid leukemia

value: Cells were harvested after 24 hours of mono-culture.


title: BMSC Transwell Co-cultured with TF-1alpha - 4 hr

description: No additional information.


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=42

description:
5445295027_B
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=42

value: lung


title: Human oral microbiome from patients with moderate periodontitis PL10


title: Human oral microbiome from patients with moderate periodontitis PL9


title: BMSC Transwell Mono-culture - 24 hr - repeat 2

description: No additional information.

source_name: BMSC Transwell Mono-culture - 24 hr


title: K562 Transwell Mono-culture - 24 hr

description: No additional information.

source_name: K562 Transwell Mono-culture - 24 hr

treatment_protocol: In-vitro treatment: CD34- chronic myeloid leukemia cell line, K562, cells were mono-cultured in a 1-um Transwell system (BD Biosciences, San Jose, CA USA). K562 cells were harvested and RNA extracted.

value: CD34- myeloid leukemia cells


title: control_6 hours_rep1 (exon-level)

description:
MCF17 treated by DMSO for 6 hours
MCF7_CTRL_n1


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=46

description:
5447354026_A
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=46

value: F


title: control_6 hours_rep3 (exon-level)

description:
MCF17 treated by DMSO for 6 hours
MCF7_CTRL_n3


title: Human oral microbiome from patients with moderate periodontitis PL8


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=38

description:
4717421101_L
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=38

value: M


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=36

description:
4717421101_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=36

value: Other


title: BMSC Transwell Co-cultured with K562 - 24 hr

description: No additional information.

source_name: Universal Human Reference RNA

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

treatment_protocol: In-vitro treatment: BMSCs from healthy donors were co-cultured with a CD34- chronic myeloid leukemia cell line, K562. A 1-um Transwell system (BD Biosciences, San Jose, CA USA) was used to maintain the cultured BMSC and K562 cell populations separate from each other. BMSC cells were harvested and RNA extracted.


title: T84_1h_ST_Rep1

scan_protocol: Agilent Feature Extraction Software (v 9.5.3.1)

value: T84 colorectal carcinoma cell line


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=39

description:
5125398047_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=39


title: K562 Transwell Co-cultured with BMSC - 24 hr

description: No additional information.

treatment_protocol: In-vitro treatment: CD34- chronic myeloid leukemia cell line, K562, cells were co-cultured with BMSCs from healthy donors. A 1-um Transwell system (BD Biosciences, San Jose, CA USA) was used to maintain the cultured BMSC and K562 cell populations separate from each other. K562 cells were harvested and RNA extracted.


title: Human oral microbiome from patients with moderate periodontitis PL4


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=35

description:
4674281014_J
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=35


title: Human oral microbiome from patients with moderate periodontitis PL7


title: K562 + BMSCs in Direct Co-culture - 10 hr

description: No additional information.

value: Cells were harvested after 10 hours of co-culture.


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=43

description:
5445295025_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=43


title: K562 + BMSCs from Separate Mono-culture - 10 hr

description: No additional information.

value: Bone marrow

value: Cells were harvested after 10 hours of mono-culture.


title: Control r7

city: Gainesville

first: M Cecilia

last: Lopez

state: FL

address: 1376 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description: Gene expression data from WBC from mice

hyb_protocol: Equal amounts of RNA from samples were labeled and hybridized on a mouse GeneChip following the protocol described in the GeneChip Expression Analysis Technical manual (Affymetrix, Santa Clara, CA).

scan_protocol: The GeneChip arrays were stained and scanned in an Affymetrix GCS 3000 7G Scanner.

data_processing: The data was normalized  using RMA. Analyzed using BRB array tools

organism: Mus musculus

source_name: Control r3

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

extract_protocol: Extraction of total RNA was performed with QIAGEN Rneasy mini kit according to the manufacturer's instructions.

treatment_protocol: Used the Cecal Ligation and Puncture model

tag: treatment

value: control

value: WBC

tag: age

value: 6-12 weeks


title: Human oral microbiome from patients with moderate periodontitis PL6


title: Human oral microbiome from patients with moderate periodontitis PL3


title: Control r8

description: Gene expression data from WBC from mice

source_name: Control r4


title: BMSC Transwell Mono-culture - 10 hr - repeat 2

description: No additional information.

source_name: BMSC Transwell Mono-culture - 10 hr

treatment_protocol: In-vitro treatment: BMSCs from healthy donors were mono-cultured in a 1-um Transwell system (BD Biosciences, San Jose, CA USA). BMSC cells were harvested and RNA extracted.

value: Bone marrow derived stromal cells (BMSC)


title: Control r6

description: Gene expression data from WBC from mice

source_name: Control r2


title: Human oral microbiome from patients with severe dental caries CH15


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=33

description:
4674281014_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=33

value: whole blood

tag: disease status

value: sepsis survivor

tag: age (years)


title: Human oral microbiome from patients with severe dental caries CH14


title: K562 Transwell Mono-culture - 10 hr

description: No additional information.

source_name: K562 Transwell Mono-culture - 10 hr

value: myeloid leukemia


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=34

description:
4674281015_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=34

tag: severity (apacheii)

tag: neutrophil proportion

value: UT


title: Control r5

description: Gene expression data from WBC from mice

source_name: Control r1


title: Human oral microbiome from patients with severe dental caries CH13


title: CLP YNG Day3 r4

description: Gene expression data from WBC from mice

source_name: CLP YNG Day3 r4

value: Cecal Ligation and Puncture model

tag: time


title: CLP YNG Day3 r3

description: Gene expression data from WBC from mice

source_name: CLP YNG Day3 r3


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=32

description:
4481649065_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=32

tag: site of infection


title: Human oral microbiome from patients with severe dental caries CH11


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=30

description:
4674281009_I
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=30

value: F

value: blood


title: CLP YNG Day3 r2

description: Gene expression data from WBC from mice

source_name: CLP YNG Day3 r2


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=52

description:
5447354040_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=52

value: lung


title: PAXgene whole blood, sepsis_survivor, Day_3, ID=31

description:
4481649092_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 3, ID=31


title: K562 + BMSCs from Separate Mono-culture - 4 hr

description: No additional information.

source_name: Universal Human Reference RNA

tag: other

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

value: CD34- myeloid leukemia cells (K562) and Bone marrow derived stromal cells (BMSC)

value: Cells were harvested after 4 hours of mono-culture.


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=54

description:
5445295021_I
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=54

tag: tissue

value: M


title: Human oral microbiome from patients with severe dental caries CH8


title: K562 Transwell Co-cultured with BMSC - 10 hr

description: No additional information.

value: Bone marrow

tag: cell type

value: CD34- myeloid leukemia cells

value: Cells were harvested after 10 hours of co-culture.


title: K562 Transwell Mono-culture - 4 hr

description: No additional information.

source_name: K562 Transwell Mono-culture - 4 hr

tag: cell line


title: BMSC Transwell Co-cultured with K562 - 10 hr

description: No additional information.


title: K562 + BMSCs in Direct Co-culture - 4 hr

description: No additional information.

tag: disease state

value: Cells were harvested after 4 hours of co-culture.


title: CLP YNG Day3 r1

description: Gene expression data from WBC from mice

source_name: CLP YNG Day3 r1

value: WBC

value: 6-12 weeks


title: Human oral microbiome from patients with severe dental caries CH9

tag: source


title: BMSC Transwell Mono-culture - 4 hr - repeat 2

description: No additional information.

source_name: BMSC Transwell Mono-culture - 4 hr

value: Bone marrow derived stromal cells (BMSC)


title: Human oral microbiome from patients with severe dental caries CH7


title: CLP YNG Day1 r4

description: Gene expression data from WBC from mice

source_name: CLP YNG Day1 r4


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=50

description:
5447354026_I
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=50

value: whole blood

value: sepsis survivor

value: Other


title: CLP YNG 2hr r4

description: Gene expression data from WBC from mice

source_name: CLP YNG 2hr r4

value: Cecal Ligation and Puncture model


title: CLP YNG Day1 r2

description: Gene expression data from WBC from mice

source_name: CLP YNG Day1 r2


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=51

description:
5447354040_B
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=51


title: Human oral microbiome from patients with severe dental caries CH5


title: TF-1 + BMSCs in Direct Co-culture - 24 hr

description: No additional information.

treatment_protocol: In-vitro treatment: AML cell line, TF-1, cells were co-cultured with BMSCs from healthy donors. The two populations were cultured together in direct contact in the same well without any membrane separation. The cells from both populations were harvested together and RNA extracted.

value: CD34+/CD38+ myeloid leukemia cells (TF-1) and Bone marrow derived stromal cells (BMSCs)

value: myeloid leukemia

value: Cells were harvested after 24 hours of co-culture.


title: K562 Transwell Co-cultured with BMSC - 4 hr

description: No additional information.

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=53

description:
5447354040_J
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=53

value: F


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=48

description:
5447354026_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=48


title: CLP YNG Day1 r1

description: Gene expression data from WBC from mice

source_name: CLP YNG Day1 r1


title: TF-1 + BMSCs from Separate Mono-culture - 24 hr

description: No additional information.

treatment_protocol: In-vitro treatment: AML cell line, TF-1, cells and BMSCs from healthy donors were cultured as separate monocultures. The cells from both populations were harvested and pooled together and RNA extracted.

value: Cells were harvested after 24 hours of mono-culture.


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=49

description:
5447354008_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=49


title: CLP YNG 2hr r3

description: Gene expression data from WBC from mice

source_name: CLP YNG 2hr r3


title: CLP YNG 2hr r1

description: Gene expression data from WBC from mice

source_name: CLP YNG 2hr r1


title: Human oral microbiome from patients with severe dental caries CH6


title: CLP YNG Day1 r3

description: Gene expression data from WBC from mice

source_name: CLP YNG Day1 r3


title: BMSC Transwell Co-cultured with K562 - 4 hr

description: No additional information.

source_name: Universal Human Reference RNA

value: Bone marrow


title: TF-1 Transwell Mono-culture - 24 hr

description: No additional information.

source_name: TF-1 Transwell Mono-culture - 24 hr

treatment_protocol: In-vitro treatment: AML cell line, TF-1, cells were mono-cultured in a 1-um Transwell system (BD Biosciences, San Jose, CA USA). TF-1 cells were harvested and RNA extracted.

value: CD34+/CD38+ myeloid leukemia cells


title: Human oral microbiome from patients with severe dental caries CH4


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=47

description:
5445295025_B
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=47

value: M


title: CLP YNG 2hr r2

description: Gene expression data from WBC from mice

source_name: CLP YNG 2hr r2


title: Human oral microbiome from patients with severe dental caries CH2


title: Human oral microbiome from patients with severe dental caries CH3


title: BMSC Transwell Mono-culture - 24 hr - repeat 1

description: No additional information.

source_name: BMSC Transwell Mono-culture - 24 hr


title: CLP OLD Day3 r4

description: Gene expression data from WBC from mice

source_name: CLP OLD Day3 r4

value: 20-24 months


title: Human oral microbiome from patients with severe dental caries CH1


title: TF-1 + BMSCs in Direct Co-culture - 10 hr

description: No additional information.

value: Cells were harvested after 10 hours of co-culture.


title: Human oral microbiome from patients with moderate dental caries CL8


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=43

description:
5445295025_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=43

value: lung


title: TF-1 Transwell Co-cultured with BMSC - 24 hr

description: No additional information.

treatment_protocol: In-vitro treatment: AML cell line, TF-1, cells were co-cultured with BMSCs from healthy donors. A 1-um Transwell system (BD Biosciences, San Jose, CA USA) was used to maintain the cultured BMSC and TF-1 cell populations separate from each other. TF-1 cells were harvested and RNA extracted.


title: Human oral microbiome from patients with moderate dental caries CL10


title: CLP OLD Day3 r3

description: Gene expression data from WBC from mice

source_name: CLP OLD Day3 r3

value: WBC


title: CLP OLD Day1 r4

description: Gene expression data from WBC from mice

source_name: CLP OLD Day1 r4


title: TF-1 Transwell Mono-culture - 10 hr

description: No additional information.

source_name: TF-1 Transwell Mono-culture - 10 hr

value: Cells were harvested after 10 hours of mono-culture.


title: Human oral microbiome from patients with moderate dental caries CL7


title: CLP OLD Day1 r3

description: Gene expression data from WBC from mice

source_name: CLP OLD Day1 r3


title: BMSC Transwell Mono-culture - 10 hr - repeat 1

description: No additional information.

source_name: BMSC Transwell Mono-culture - 10 hr

value: Bone marrow derived stromal cells (BMSC)


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=45

description:
5447354008_B
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=45

value: whole blood

value: sepsis survivor

value: blood


title: Human oral microbiome from patients with moderate dental caries CL3


title: BMSC Transwell Co-cultured with TF-1 - 24 hr

description: No additional information.

treatment_protocol: In-vitro treatment: BMSCs from healthy donors were co-cultured with AML cell line, TF-1, with phenotype CD34+/CD38+. A 1-um Transwell system (BD Biosciences, San Jose, CA USA) was used to maintain the cultured BMSC and TF-1 cell populations separate from each other. BMSC cells were harvested and RNA extracted.


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=42

description:
5445295027_A
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=42


title: TF-1 + BMSCs from Separate Mono-culture - 10 hr

description: No additional information.

value: CD34+/CD38+ myeloid leukemia cells (TF-1) and Bone marrow derived stromal cells (BMSCs)

value: myeloid leukemia


title: TF-1 Transwell Co-cultured with BMSC - 10 hr

description: No additional information.

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=39

description:
5125398047_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=39

value: F


title: CLP OLD Day3 r1

description: Gene expression data from WBC from mice

source_name: CLP OLD Day3 r1

value: Cecal Ligation and Puncture model


title: Human oral microbiome from patients with moderate dental caries CL6


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=46

description:
5447354008_L
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=46


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=41

description:
5125398047_I
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=41


title: CLP OLD Day3 r5

description: Gene expression data from WBC from mice

source_name: CLP OLD Day3 r5


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=40

description:
5125398047_B
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=40

value: UT


title: Human oral microbiome from patients with moderate dental caries CL17


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=38

description:
4717421101_K
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=38


title: Human oral microbiome from patients with moderate dental caries CL15


title: CLP OLD Day3 r2

description: Gene expression data from WBC from mice

source_name: CLP OLD Day3 r2


title: Human oral microbiome from patients with moderate dental caries CL14


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=35

description:
4674281014_K
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=35


title: CLP OLD Day1 r1

description: Gene expression data from WBC from mice

source_name: CLP OLD Day1 r1


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=36

description:
4717421101_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=36

value: Other


title: Human oral microbiome from patients with moderate dental caries CL13


title: Human oral microbiome from patients with moderate dental caries CL16


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=37

description:
5125398041_K
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=37

value: M


title: TF-1 + BMSCs in Direct Co-culture - 4 hr

description: No additional information.

source_name: Universal Human Reference RNA

value: Bone marrow

value: Cells were harvested after 4 hours of co-culture.


title: TF-1 Transwell Mono-culture - 4 hr

description: No additional information.

source_name: TF-1 Transwell Mono-culture - 4 hr

value: CD34+/CD38+ myeloid leukemia cells

value: Cells were harvested after 4 hours of mono-culture.


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=34

description:
4674281015_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=34


title: CLP OLD Day1 r2

description: Gene expression data from WBC from mice

source_name: CLP OLD Day1 r2

value: WBC

value: 20-24 months


title: Human oral microbiome from patients with moderate dental caries CL11


title: CLP OLD 2hr r4

description: Gene expression data from WBC from mice

source_name: CLP OLD 2hr r4


title: BMSC Transwell Mono-culture - 4 hr - repeat 1

description: No additional information.

source_name: BMSC Transwell Mono-culture - 4 hr

value: Bone marrow derived stromal cells (BMSC)


title: BMSC Transwell Co-cultured with TF-1 - 10 hr

description: No additional information.

value: Cells were harvested after 10 hours of co-culture.


title: TF-1 + BMSCs from Separate Mono-culture - 4 hr

description: No additional information.


title: CLP OLD 2hr r3

description: Gene expression data from WBC from mice

source_name: CLP OLD 2hr r3


title: TF-1 Transwell Co-cultured with BMSC - 4 hr

description: No additional information.


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=33

description:
4674281014_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=33

value: whole blood

value: sepsis survivor

value: lung


title: CLP OLD 2hr r2

description: Gene expression data from WBC from mice

source_name: CLP OLD 2hr r2


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=32

description:
4481649065_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=32


title: Human oral microbiome from healthy individuals H16


title: Human oral microbiome from patients with moderate dental caries CL1


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=31

description:
4481649092_B
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=31


title: Human oral microbiome from healthy individuals H15


title: Hyper 4

city: ottawa

first: hongyan

last: dong

address: 50 colombine Dr.

country: Canada

institute: health canada

hyb_protocol: Biotin-labeled cRNA was purified using the GeneChip cleanup module prior to fragmenting to a size of 35-200 bases by incubating at 94 °C for 35 min in fragmentation buffer.  Fragmented cRNA was hybridized to the arrays for 16 hours at 45 °C .

scan_protocol: After hybridization, arrays were washed using an Affymetrix fluidics station and stained with streptavidin-phycoerythrin (10 mg/ml, Molecular Probes). Washed arrays were scanned on an Affymetrix GeneChip scanner 3000.  Scanned output files were visually inspected for hybridization artifacts.

data_processing:
MAS 5.0
contents of CHP files: Algorithm: ExpressionStat 5.0
All pre-processing of the data was conducted using the R package. The data were normalized by robust multi-array average (RMA) using the ReadAffy function in the Affy R library (Irizarry RA et al., 2003). The Fs statistic (Cui X et al., 2005), a shrinkage estimator, was used for the gene-specific variance components, and the associated p-values (unadjusted p) for all the statistical tests were estimated using the permutation method (30,000 permutations with residual shuffling). These p-values were then adjusted for multiple comparisons using the false discovery rate (FDR) approach (Benjamini Y et al., 2001). The least squares mean (Goodnight JH HW, 1978; Searle SR SF, Milliken GA, 1980), a function of the model parameters, was used to estimate the fold-change for each pairwise comparison of interest (control versus each of the three treatment groups: hyper, hypo, and hypo+).

source_name: mouse fetal cerebral cortex on GD16 injected with Thyroid hormone 12 hours before sacrifice

label_protocol: The Yale Center for the Neuroscience Microarray Consortium carried out the Affymetrix microarray analysis using The GeneChip Rat Genome 230 2.0 Array.  Preparation of labeled cRNA for hybridization onto Affymetrix GeneChips followed the recommended Affymetrix protocol.  Briefly, double stranded cDNA was synthesized from 1 to 5 ug of total RNA by using a Superscript Choice System (Invitrogen), with an HPLC-purified oligo (dT) 24 primer containing a T7 RNA polymerase promoter sequence at the 5’-end (Proligo LLC. Boulder, CO). The second cDNA strand was synthesized by using E. Coli DNA polymerase I, RNase H and DNA ligase.  Labeled cRNA was generated from cDNA by in vitro transcription using a GeneChip IVT labeling kit (Affymetrix Inc.) following the manufacturer’s instructions and incorporating biotinylated synthetic analog as pseudouridine reagent, a reaction mediated by MEGAscript T7 RNA Polymerase.

extract_protocol: Dams were killed by exposure to CO2. Fetuses were dissected from the uterine horn and embryonic membranes then frozen on pulverized dry ice. Tissue samples were taken from the fetuses to determine sex using PCR for SRY (Yang J and RT Zoeller, 2002). Fetal cerebral cortices were removed from each mouse and used for microarray and RT-PCR analysis. Total RNA was extracted from half cortices of individual female fetuses using RNeasy Lipid tissue Mini kits (Qiagen, Germantown, MD) according to the manufacturer's instructions.  The quality of total RNA was evaluated by A260/A280 ratio (found to be at least 1.8 for each sample) and by electrophoresis on the Agilent Bioanalyzer.

treatment_protocol: Timed-pregnant C57BL/6 mice (n=20; Harlan, Indianapolis, IN) arrived on gestational day (GD) 11 and were housed individually in plastic cages under a 12:12 light cycle (0600 h–1800 h) with food available ad libitum. Mice were divided randomly into one of 4 groups (control, hypo, hypo+ and hyper; 5 per group) . Mice in the control and hyper groups were provided with fresh drinking water containing 2% sucrose from GD 13 to GD 16 until sacrifice. Mice in hypo and hypo+ were provided with fresh drinking water daily containing 1% Perchlorate (Per) and 0.025% Methimazole (MMI) supplemented with 2% sucrose (to mask bitterness) from GD 13 to sacrifice on GD 16. Twelve hours prior to sacrifice on GD 16 all mice received a single subcutaneous injection. Control and hypo mice received vehicle (0.9% saline in 100 µl volume); the hypo+ group received 25.0 µg/100g body weight thyroxine (T4) with 2.5 µg/100g body weight T3 to restore a physiological level of TH; the hyper group received 100.0 µg/100g body weight T4 with 10.0 µg/100g body weight T3 to model hyperthyroidism.

tag: strain

value: provided with fresh drinking water containing 2% sucrose from GD 13 to GD 16 until sacrifice +  100.0 µg/100g body weight T4 with 10.0 µg/100g body weight T3 to model hyperthyroidism

value: Fetal cerebral cortex

tag: genotype

value: wild type

value: gestational day 16


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=54

description:
5445295021_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=54

tag: gender


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=53

description:
5447354040_I
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=53

value: F

value: Other


title: Human oral microbiome from healthy individuals H13


title: CLP OLD 2hr r1

description: Gene expression data from WBC from mice

source_name: CLP OLD 2hr r1

tag: treatment

value: Cecal Ligation and Puncture model


title: Human oral microbiome from healthy individuals H12


title: Hyper 3

tag: age


title: Human oral microbiome from healthy individuals H14


title: Hyper 2


title: Human oral microbiome from healthy individuals H11


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=51

description:
5447354040_A
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=51

tag: disease status

value: M


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=49

description:
5447354008_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=49

tag: age (years)


title: Human oral microbiome from healthy individuals H10


title: Hypo+ 4

source_name: mouse fetal cerebral cortex on GD16 treated with PTU for 3 days and injected with thyroid hormone 12 hours before sacrifice

value: provided with fresh drinking water daily containing 1% Perchlorate (Per) and 0.025% Methimazole (MMI) supplemented with 2% sucrose (to mask bitterness) from GD 13 to sacrifice on GD 16 +  25.0 µg/100g body weight thyroxine (T4) with 2.5 µg/100g body weight T3 to restore a physiological level of TH


title: Human oral microbiome from healthy individuals H6


title: Hypo+ 5


title: Human oral microbiome from healthy individuals H5


title: Hyper 1


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=52

description:
5447354040_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=52

tag: severity (apacheii)


title: BMSC Transwell Co-cultured with TF-1 - 4 hr

description: No additional information.

source_name: Universal Human Reference RNA

value: Stratagene(TM)UHR RNA Sample Pooling:Equal quantities of total RNA from each cell line (brain, breast, B-lymphocyte, cervix, liver, liposarcoma, macrophages, skin, testis, Y-lymphocyte) were pooled together.

value: Bone marrow

value: Cells were harvested after 4 hours of co-culture.


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=50

description:
5447354026_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=50

tag: neutrophil proportion


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=48

description:
5447354026_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=48


title: Human oral microbiome from healthy individuals H4


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=45

description:
5447354008_A
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=45

value: blood


title: Human oral microbiome from healthy individuals H2


title: Hypo+ 3


title: Human gut microbiome from healthy individuals with alcohol abuse CD12


title: Human gut microbiome from healthy individuals with alcohol abuse CD13


title: Hypo 5

source_name: mouse fetal cerebral cortex on GD16 treated with PTU for 3 days

value: provided with fresh drinking water daily containing 1% Perchlorate (Per) and 0.025% Methimazole (MMI) supplemented with 2% sucrose (to mask bitterness) from GD 13 to sacrifice on GD 16 + vehicle


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=44

description:
5445295006_L
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=44

value: whole blood


title: Human gut microbiome from healthy individuals with alcohol abuse CD14


title: Human oral microbiome from healthy individuals H1


title: Hypo 4


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=46

description:
5447354008_K
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=46

value: sepsis survivor


title: Hypo+ 1


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=43

description:
5445295006_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=43

value: lung