title: hESC (H9) p34, P4 after conversion to a naïve state with L3i

description: Individual sample

source_name: H9 human Embryonic Stem Cells, Passage 34 (NIH Code WA09), P4 after conversion to a naïve state with L3i


title: LP-1/Cfz_rep3_261888

status: Public on Sep 13 2016

type: RNA

city: Washington

first: Robert

last: Hawley

state: DC

address: 2300 I Street NW, Suite 431

department: Anatomy and Regenerative Biology

country: USA

institute: George Washington University

description:
Gene expression data from LP-1/Cfz multiple myeloma cells resistant to 12 nM carfilzomib
SAMPLE 1.3

hyb_protocol: Hybridization of cRNA on Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays was performed by Expression Analysis.

scan_protocol: Scanning of GeneChip arrays was performed by Expression Analysis.

data_processing: The data were analyzed with GeneSpring software (Agilent Technologies) using default settings and the RMA normalization and summarization algorithm.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA was prepared by Expression Analysis (Durham, NC).

growth_protocol: Cells for gene expression profiling were cultured in RPMI 1640 with GlutaMAX (Life Technologies) supplemented with 4% fetal bovine serum.

extract_protocol: Total RNA was isolated with the miRNeasy mini kit (Qiagen).

treatment_protocol: LP-1/Cfz cells were profiled for gene expression after 1 week of growth in the absence of carfilzomib together with parental LP-1 cells which had not been selected in the drug.

tag: cell line


title: TNBC tumor FFPE block 51689-92

city: Gliwice

first: Aleksandra

last: Pfeifer

address: Wybrzeze Armii Krajowej 15

country: Poland

institute: MSC Memorial Cancer Center and Institute of Oncology

description:
9284936060_I
FBB-254

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol on Illumina iScan microarray scanner

data_processing: The data were exported from GenomeStudio and normalised using quantile normalisation with the beadarray library in R

source_name: triple negative breast cancer, tumor area, FFPE block

label_protocol: Whole-Genome DASL (cDNA-mediated Annealing, Selection, Extension, and Ligation) Gene Expression Assay (Illumina, San Diego, California) was used, carried out as per manufacturer’s instructions. Two hundred nanograms of total RNA was used in the procedure.

extract_protocol: RNA isolation was performed using the QIAGEN RNeasy FFPE Kit (Qiagen, Hilden, Germany), in accordance with the manufacturer’s protocol. The RNeasy FFPE kit includes traditional RNeasy MinElute series columns for RNA purification, and additionally gDNA Eliminator columns, which allow for the removal from the sample of genomic DNA that contaminates the isolated RNA. The blocks were cut into 5 μm-thick sections. In RNA isolation, 5 sections were used per one examination. The material was deparaffinized using xylene and, after supernatant removal, rinsed in alcohol. RNA concentration was evaluated using the Nanodrop ND-1000 microspectrophotometer. No routine RNA quality analysis was carried out.

tag: patient group

value: TNBC patient without brain metastasis (BM)

tag: patient age at breast cancer diagnosis

tag: disease stage at diagnosis

tag: tumor grade

tag: patient age at metastatic disease

tag: location of metastatic disease

value: other than central nervous system


title: TNBC tumor FFPE block 8309 B/06

description:
9284936060_F
FBB-141


title: nonviral 4F stromal primed GCSF-mobilized peripheral blood iPSC clone E29C3 p7 [FigS4]

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

state: MD

address: 733 N. Broadway

department: Oncology

institute: Johns Hopkins School of Medicine

description: Individual sample

hyb_protocol: For array assay, 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed. Illumina HumanHT-12 V4.0 expression beadchips were used for all analyses in this series.

scan_protocol: Fluorescent signals were obtained by scanning with the iScan System.

data_processing: Data were extracted with Gene Expression Module 1.0.6 in GenomeStudio 1.0.2 and signal intensities from multiple chips comprising this single series were quantile normalized without background subtraction to obtain normalized data as deposited.

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed GCSF-mobilized peripheral blood iPSC clone E29C3 passage 7

label_protocol: 500 ng total RNA from each sample was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) as described in the instruction manual.

extract_protocol: Total RNA was prepared as described in the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion. RNA quality was assessed by Nanodrop-1000 spectrometer for OD260/280 and OD260/230 ratio and Bioanalyzer (Agilent Technologies).

tag: cell type

tag: sample type

value: non-integrated stromal primed GCSF-mobilized peripheral blood iPSC generated in the Zambidis laboratory


title: TNBC tumor FFPE block 13453/03 (1)

description:
9284936060_C
FBB-069


title: nonviral 7F stromal primed cord blood iPSC clone 19.11 p17 [FigS4]

description: Individual sample

source_name: nonviral 7F stromal primed cord blood iPSC clone 19.11 passage 17

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory


title: TNBC tumor FFPE block 50363/05

description:
9284936060_E
FBB-154

value: TNBC patient with brain metastasis (BM)

value: with brain metastases


title: nonviral 4F non-stromal primed GCSF-mobilized peripheral blood iPSC clone E29C12 p7 [FigS4]

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) non-stromal primed GCSF-mobilized peripheral blood iPSC clone E29C12 passage 7

value: non-integrated non-stromal primed GCSF-mobilized peripheral blood iPSC generated in the Zambidis laboratory


title: TNBC tumor FFPE block 02-6883

description:
9284936003_L
FBB-324


title: TNBC tumor FFPE block 3842 B/03

description:
9284936060_B
FBB-148


title: nonviral 4F stromal primed GCSF-mobilized peripheral blood iPSC clone E29C2 p7 [FigS4]

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed GCSF-mobilized peripheral blood iPSC clone E29C2 passage 7


title: nonviral 7F non-stromal primed cord blood iPSC clone iCB9 p18 [FigS4]

description: Individual sample

source_name: nonviral 7F non-stromal primed cord blood iPSC clone iCB9 passage 18

value: Provided by I.I. Slukvin (U. Wisconsin). Originally derived in Hu et al. Blood 117(14):e109-19. (2011)


title: TNBC tumor FFPE block 21570-2

description:
9284936003_I
FBB-252


title: nonviral 4F non-stromal primed GCSF-mobilized peripheral blood iPSC clone E29C10 p7 [FigS4]

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) non-stromal primed GCSF-mobilized peripheral blood iPSC clone E29C10 passage 7


title: TNBC tumor FFPE block 18645B/09

description:
9284936060_D
FBB-419


title: nonviral 4F non-stromal primed GCSF-mobilized peripheral blood iPSC clone E29C7 p7 [FigS4]

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) non-stromal primed GCSF-mobilized peripheral blood iPSC clone E29C7 passage 7


title: nonviral 7F stromal primed cord blood iPSC clone 6.2 p18 [FigS4]

description: Individual sample

source_name: nonviral 7F stromal primed cord blood iPSC clone 6.2 passage 18


title: nonviral 4F non-stromal primed cord blood iPSC clone E24C1 p17 [FigS4]

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) non-stromal primed cord blood iPSC clone E24C1 passage 17

value: non-integrated non-stromal primed cord blood iPSC generated in the Zambidis laboratory


title: TNBC tumor FFPE block 17535/07 (1)

description:
9284936060_A
FBB-044


title: TNBC tumor FFPE block 2764

description:
9284936003_F
FBB-203


title: nonviral 7F non-stromal primed cord blood iPSC clone iCB8 p19 [FigS4]

description: Individual sample

source_name: nonviral 7F non-stromal primed cord blood iPSC clone iCB8 passage 19


title: TNBC tumor FFPE block 37216/10

description:
9284936003_E
FBB-191


title: nonviral 7F stromal primed cord blood iPSC clone 6.13 p22 [FigS4]

description: Individual sample

source_name: nonviral 7F stromal primed cord blood iPSC clone 6.13 passage 22


title: TNBC tumor FFPE block 26126/08

description:
9284936003_D
FBB-149


title: nonviral 7F non-stromal primed cord blood iPSC clone iCB 2-5 p18 [FigS4]

description: Individual sample

source_name: nonviral 7F non-stromal primed cord blood iPSC clone iCB2-5 passage 18


title: nonviral 4F non-stromal primed cord blood iPSC clone E20C2 p18 [FigS4]

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) non-stromal primed cord blood iPSC clone E20C2 passage 18


title: nonviral 4F stromal primed cord blood iPSC clone E12C5 p19 [FigS4]

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E12C5 passage 19


title: TNBC tumor FFPE block 20223/09 (1)

description:
9284936003_C
FBB-055


title: nonviral 4F stromal primed cord blood iPSC clone E5C3 p18 [FigS4]

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E5C3 passage 18


title: TNBC tumor FFPE block 64879-84

description:
9284936003_H
FBB-248


title: TNBC tumor FFPE block 4097 D/09

description:
9284936003_G
FBB-209


title: TNBC tumor FFPE block 30258/09

description:
9284936003_J
FBB-283


title: TNBC tumor FFPE block 26646/06

description:
9284936003_K
FBB-298


title: nonviral 4F stromal primed cord blood iPSC clone E17C6 p21 [FigS4]

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E17C6 passage 21


title: Cord Blood CD34+ progenitors Day zero, Sample 5 [FigS4]

description: Individual sample

source_name: Cord Blood CD34+ Day Zero progenitors, treated as described, Sample 5

value: Cord Blood CD34+ Day Zero progenitors, Sample 5

value: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO, and then harvested


title: hESC (H7) p38 [FigS4]

description: Individual sample

source_name: H7 human Embryonic Stem Cells, Passage 38 (NIH Code WA07)

value: Undifferentiated hESC


title: hESC (ESO3) p84 [FigS4]

description: Individual sample

source_name: ES03 human Embryonic Stem Cells, Passage 84 (ES Cell International)


title: TNBC tumor FFPE block 985565

description:
9284936003_B
FBB-186

source_name: triple negative breast cancer, tumor area, FFPE block


title: Cord Blood CD34+ progenitors Day zero, Sample 4 [FigS4]

description: Individual sample

source_name: Cord Blood CD34+ Day Zero progenitors, treated as described, Sample 4

value: Cord Blood CD34+ Day Zero progenitors, Sample 4


title: nonviral 4F non-stromal primed cord blood iPSC clone E17C1 p9 [FigS4]

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) non-stromal primed cord blood iPSC clone E17C1 passage 9


title: Cord Blood CD34+ progenitors Day zero, Sample 3 [FigS4]

description: Individual sample

source_name: Cord Blood CD34+ Day Zero progenitors, treated as described, Sample 3

value: Cord Blood CD34+ Day Zero progenitors, Sample 3


title: TNBC tumor FFPE block 04-4569

description:
9271668096_L
FBB-320


title: TNBC tumor FFPE block 17208 B/09

description:
9271668096_K
FBB-157


title: Fibroblast Day zero, Sample 3 [FigS4]

description: Individual sample

source_name: adult fibroblasts, Coriell Institute, Cat # AG07714, treated as described

value: adult fibroblasts

value: Fibroblasts passaged 2-3 days prior to day 0 and then harvested on day zero


title: TNBC tumor FFPE block 993/06 (1)

description:
9284936003_A
FBB-033


title: hESC (ESO3) p84

description: Individual sample

value: ES03 human Embryonic Stem Cells, Passage 84 (ES Cell International)


title: Fibroblast Day zero, Sample 2 [FigS4]

description: Individual sample


title: TNBC tumor FFPE block 28238/08

description:
9271668096_E
FBB-152


title: TNBC tumor FFPE block 1890-5/04

description:
9271668096_J
FBB-259

value: TNBC patient without brain metastasis (BM)


title: Cord Blood CD34+ progenitors Day zero, Sample 2 [FigS4]

description: Individual sample

source_name: Cord Blood CD34+ Day Zero progenitors, treated as described, Sample 2

value: Cord Blood CD34+ Day Zero progenitors, Sample 2


title: hESC (H9) p60 [FigS4]

description: Individual sample

source_name: H9 human Embryonic Stem Cells, Passage 60 (NIH Code WA09)


title: Fibroblast Day zero, Sample 1 [FigS4]

description: Individual sample


title: TNBC tumor FFPE block 8550C/06

description:
9271668096_F
FBB-360


title: Cord Blood CD34+ progenitors Day zero, Sample 1 [FigS4]

description: Individual sample

source_name: Cord Blood CD34+ Day Zero progenitors, treated as described, Sample 1

value: Cord Blood CD34+ Day Zero progenitors, Sample 1


title: TNBC tumor FFPE block 52235/02

description:
9271668096_D
FBB-153


title: TNBC tumor FFPE block 19026/06 (1)

description:
9271668096_I
FBB-054

value: other than central nervous system


title: hESC (H7) p38

description: Individual sample

value: H7 human Embryonic Stem Cells, Passage 38 (NIH Code WA07)


title: TNBC tumor FFPE block 0419755

description:
9271668086_L
FBB-309


title: TNBC tumor FFPE block 29061/06 (1)

description:
9271668096_A
FBB-051


title: TNBC tumor FFPE block 715147

description:
9271668096_B
FBB-416


title: TNBC tumor FFPE block 32808/09

description:
9271668096_G
FBB-373


title: TNBC tumor FFPE block 16474B/09

description:
9271668096_H
FBB-156

value: TNBC patient with brain metastasis (BM)

value: with brain metastases


title: TNBC tumor FFPE block 140005/05 (1)

description:
9271668096_C
FBB-096


title: hESC (H9) p60

description: Individual sample

value: H9 human Embryonic Stem Cells, Passage 60 (NIH Code WA09)


title: TNBC tumor FFPE block 11957/07

description:
9271668086_K
FBB-299


title: TNBC tumor FFPE block 02-9996

description:
9271668086_J
FBB-317


title: nonviral 7F stromal primed cord blood iPSC clone 6.13 p22

description: Individual sample

source_name: nonviral 7F stromal primed cord blood iPSC clone 6.13 passage 22

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory


title: TNBC tumor FFPE block 93229

description:
9271668086_I
FBB-265


title: nonviral 7F non-stromal primed cord blood iPSC clone iCB 2-5 p18

description: Individual sample

source_name: nonviral 7F non-stromal primed cord blood iPSC clone iCB2-5 passage 18

value: Provided by I.I. Slukvin (U. Wisconsin). Originally derived in Hu et al. Blood 117(14):e109-19. (2011)


title: nonviral 7F non-stromal primed cord blood iPSC clone iCB8 p19

description: Individual sample

source_name: nonviral 7F non-stromal primed cord blood iPSC clone iCB8 passage 19


title: TNBC tumor FFPE block 12883 B/05

description:
9271668086_G
FBB-143


title: nonviral 4F stromal primed cord blood iPSC clone E17C6 p21

description: Individual sample

value: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E17C6 passage 21


title: nonviral 7F stromal primed cord blood iPSC clone 6.2 p18

description: Individual sample

source_name: nonviral 7F stromal primed cord blood iPSC clone 6.2 passage 18


title: TNBC tumor FFPE block 805863

description:
9271668086_D
FBB-407


title: nonviral 4F stromal primed cord blood iPSC clone E5C3 p18

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E5C3 passage 18


title: TNBC tumor FFPE block 46370-2

description:
9271668086_H
FBB-263


title: nonviral 7F stromal primed cord blood iPSC clone 19.11 p17

description: Individual sample

source_name: nonviral 7F stromal primed cord blood iPSC clone 19.11 passage 17


title: Cord Blood Day 23 +4F +BMSC, Experiment 3

description: Individual sample

source_name: neonatal cord blood CD34+ cells, treated as described

value: neonatal cord blood CD34+ cells

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) on Day zero; co-cultured with BMSC from day zero to +3, then maintained on MEF until day 23, and then harvested


title: nonviral 4F non-stromal primed cord blood iPSC clone E24C1 p17

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) non-stromal primed cord blood iPSC clone E24C1 passage 17

value: non-integrated non-stromal primed cord blood iPSC generated in the Zambidis laboratory


title: Cord Blood Day 23 +4F +BMSC, Experiment 1

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) episome on Day zero; co-cultured with BMSC from day zero to +3, then maintained on MEF until day 23, and then harvested


title: nonviral 4F stromal primed cord blood iPSC clone E12C5 p19

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E12C5 passage 19


title: TNBC tumor FFPE block 13718 B/09

description:
9271668086_F
FBB-159

source_name: triple negative breast cancer, tumor area, FFPE block


title: TNBC tumor FFPE block 778/06 (1)

description:
9271668086_C
FBB-045


title: nonviral 4F non-stromal primed cord blood iPSC clone E20C2 p18

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) non-stromal primed cord blood iPSC clone E20C2 passage 18


title: Cord Blood Day 23 +4F -BMSC, Experiment 3

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) episome on Day zero; co-cultured without BMSC from day zero to +3, then maintained on MEF until day 23, and then harvested


title: TNBC tumor FFPE block 1571/07 (1)

description:
9271668086_A
FBB-041


title: nonviral 4F non-stromal primed cord blood iPSC clone E17C1 p9

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) non-stromal primed cord blood iPSC clone E17C1 passage 9


title: TNBC tumor FFPE block 973780A

description:
9271668086_B
FBB-426


title: TNBC tumor FFPE block 246/08

description:
9240300088_H
FBB-206


title: TNBC tumor FFPE block 02-14343

description:
9240300088_J
FBB-319


title: TNBC tumor FFPE block 57818-19/08

description:
9271668086_E
FBB-372


title: TNBC tumor FFPE block 05-15162

description:
9240300088_L
FBB-326


title: nonviral 7F non-stromal primed cord blood iPSC clone iCB9 p18

description: Individual sample

source_name: nonviral 7F non-stromal primed cord blood iPSC clone iCB9 passage 18


title: TNBC tumor FFPE block 00-19011

description:
9240300088_K
FBB-316


title: Cord Blood Day 23 +4F +BMSC, Experiment 2

description: Individual sample


title: TNBC tumor FFPE block 16157 B/03

description:
9240300088_G
FBB-201


title: Cord Blood Day 23 +4F -BMSC, Experiment 2

description: Individual sample


title: TNBC tumor FFPE block 354612

description:
9240300088_I
FBB-261


title: Cord Blood Day +3 +4F, +BMSC, Experiment 3

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) on Day zero; co-cultured with BMSC from day zero to +3, then harvested


title: TNBC tumor FFPE block 12213B/03

description:
9240300088_D
FBB-368

value: TNBC patient without brain metastasis (BM)


title: Cord Blood Day +3 +4F, no BMSC, Experiment 2

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) on Day zero; co-cultured without BMSC from day zero to +3, then harvested


title: TNBC tumor FFPE block 3173B/06

description:
9240300088_E
FBB-362


title: TNBC tumor FFPE block 6216/11

description:
9240300088_B
FBB-397


title: TNBC tumor FFPE block 379166-9

description:
9240300080_K
FBB-246


title: TNBC tumor FFPE block 29617/08 (1)

description:
9240300088_A
FBB-060


title: Cord Blood Day +3 +4F, no BMSC, Experiment 3

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) on Day zero; co-cultured without BMSC from day zero to +3, then harvested


title: Cord Blood Day +3 no 4F, +BMSC, Experiment 3

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero; co-cultured with BMSC from day zero to +3, then harvested


title: TNBC tumor FFPE block 33649/09

description:
9240300080_J
FBB-281

value: other than central nervous system


title: TNBC tumor FFPE block 906-7/93

description:
9240300088_F
FBB-197

value: TNBC patient with brain metastasis (BM)


title: Cord Blood Day +3 no 4F, +BMSC, Experiment 2

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero; co-cultured with BMSC from day zero to +3, then harvested


title: Cord Blood Day +3 +4F, no BMSC, Experiment 1

description: Individual sample


title: TNBC tumor FFPE block 31083/08 (1)

description:
9240300088_C
FBB-059


title: Cord Blood Day zero, Experiment 5

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO, and then harvested


title: Cord Blood Day +3 no 4F, no BMSC, Experiment 3

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero; co-cultured without BMSC from day zero to +3, then harvested


title: TNBC tumor FFPE block 31251/02

description:
9240300080_H
FBB-239


title: TNBC tumor FFPE block 5998B/06

description:
9240300080_E
FBB-140

value: with brain metastases


title: Cord Blood Day +3 +4F, +BMSC, Experiment 2

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with 4F (SOKM) on Day zero; co-cultured with BMSC from day zero to +3, then harvested


title: Cord Blood Day +3 +4F, +BMSC, Experiment 1

description: Individual sample

value: neonatal cord blood CD34+ cells


title: Cord Blood Day +3 no 4F, no BMSC, Experiment 1

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero (D0); co-cultured without BMSC from day zero to +3, then harvested


title: Cord Blood Day +3 no 4F, no BMSC, Experiment 2

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero; co-cultured without BMSC from day zero to +3, then harvested


title: TNBC tumor FFPE block 12294B/07

description:
9240300080_G
FBB-138


title: TNBC tumor FFPE block 05-11540

description:
9240300080_L
FBB-323


title: TNBC tumor FFPE block 601/32502/02

description:
9240300080_I
FBB-225


title: TNBC tumor FFPE block 30778/11

description:
9240300080_F
FBB-242


title: Cord Blood Day +3 no 4F, +BMSC, Experiment 1

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO; nucleofected with empty vector on Day zero (D0); co-cultured with BMSC from day zero to +3, then harvested


title: 3D7-A clone E5, 45h post-invasion cDNA_2

city: New York

first: Bjorn

middle: FC

last: Kafsack

state: NY

address: 1300 York Avenue

department: Microbiology & Immunology

institute: Weill Cornell Medicine

description:
paired with ∆ap2g timecourse
Shared cDNA reference pool

hyb_protocol: See Kafsack et al. Malaria J 2012 (PMID: 22681930 ) and Painter et al. Methods Mol Biol 2013 (PMID: 22990780) for detailed methods

data_processing: Normalization was perfomed using Agilent Feature Extractor 9.5.3.1 GE2-v5_95_Feb07_no_spikein protocol, Please see array headers for detailed settings. Both raw and normalized single color data are included in the submission.

organism: Plasmodium falciparum

source_name: 3D7-A clone E5, 45h post-invasion cDNA

growth_protocol: Parasites were double synchronized and used to intiate cultures at ~10% parasitemia, media was changed every 12h

tag: strain

tag: timepoint

value: 45h post-invasion

source_name: Shared cDNA reference pool

tag: control type

value: cDNA reference pool


title: Cord Blood Day zero, Experiment 4

description: Individual sample


title: Cord Blood Day zero, Experiment 2

description: Individual sample

value: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO, and then harvested


title: TNBC tumor FFPE block 12339/12

description:
9240300080_D
FBB-131

value: TNBC patient without brain metastasis (BM)


title: 3D7-A clone E5, 39h post-invasion cDNA_2

scan_protocol: See Kafsack et al. Malaria J 2012 (PMID: 22681930 ) and Painter et al. Methods Mol Biol 2013 (PMID: 22990780) for detailed methods

source_name: 3D7-A clone E5, 39h post-invasion cDNA

value: 39h post-invasion


title: 3D7-A clone E5, 27h post-invasion cDNA_2

source_name: 3D7-A clone E5, 27h post-invasion cDNA

label_protocol: See Kafsack et al. Malaria J 2012 (PMID: 22681930 ) and Painter et al. Methods Mol Biol 2013 (PMID: 22990780) for detailed methods

value: 27h post-invasion


title: TNBC tumor FFPE block 427/04 (1)

description:
9240300080_C
FBB-052

value: other than central nervous system


title: Cord Blood Day zero, Experiment 1

description: Individual sample


title: Fibroblast Day zero, Experiment 3

description: Individual sample

source_name: adult fibroblasts, Coriell Institute, Cat # AG07714, treated as described

value: adult fibroblasts

value: Fibroblasts passaged 2-3 days prior to day 0 and then harvested on day zero


title: 3D7-A clone E5, 9h post-invasion cDNA_2

source_name: 3D7-A clone E5, 9h post-invasion cDNA

extract_protocol: See Kafsack et al. Malaria J 2012 (PMID: 22681930 ) and Painter et al. Methods Mol Biol 2013 (PMID: 22990780) for detailed methods

value: 9h post-invasion


title: TNBC tumor FFPE block 1678/04 (1)

description:
9240300080_A
FBB-028

value: TNBC patient with brain metastasis (BM)


title: Cord Blood Day -3, Experiment 2

description: Individual sample

value: Cord blood CD34+ cells harvested immediately after thawing


title: 3D7-A clone E5, 3h post-invasion cDNA_2

source_name: 3D7-A clone E5, 3h post-invasion cDNA

value: 3h post-invasion


title: 3D7-A clone E5, 21h post-invasion cDNA_2

source_name: 3D7-A clone E5, 21h post-invasion cDNA

value: 21h post-invasion


title: 3D7-A clone E5, 15h post-invasion cDNA_2

source_name: 3D7-A clone E5, 15h post-invasion cDNA

value: 15h post-invasion


title: Adult Fibroblasts Sample 2 DNA Methylome

type: genomic

description: Individual sample

hyb_protocol: Bisulphite-converted (EZ DNA methylation kit) DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using the standard Illumina protocol.

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

data_processing: Data were extracted with Methylation Module in GenomeStudio to obtain signal intensities from multiple chips comprising this single series.

label: Cy5, Cy3

molecule: genomic DNA

source_name: Adult Fibroblasts Sample 2

label_protocol: Standard Illumina protocol.

extract_protocol: Phenol-chloroform extraction.

value: Adult Fibroblasts Sample 2

value: From Coriell Institute, Cat # AG07714


title: 3D7-A clone E5, 33h post-invasion cDNA_2

source_name: 3D7-A clone E5, 33h post-invasion cDNA

value: 33h post-invasion


title: hESC (H9) p55 DNA Methylome

description: Individual sample

source_name: H9 human Embryonic Stem Cells, Passage 55 (NIH Code WA09)

tag: passage

value: Undifferentiated hESC


title: hESC (H1) p36 DNA Methylome

description: Individual sample

source_name: H1 human Embryonic Stem Cells, Passage 36 (NIH Code WA01)


title: Cord Blood Day zero, Experiment 3

description: Individual sample

source_name: neonatal cord blood CD34+ cells, treated as described

value: neonatal cord blood CD34+ cells

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO, and then harvested


title: Fibroblast Day+3 +4F Experiment 2

description: Individual sample

value: Fibroblasts passaged 2-3 days prior to day zero, nucleofected with 4F (SOKM) on day zero, and then harvested on day +3


title: Cord Blood Day -3, Experiment 1

description: Individual sample

value: Cord blood CD34+ cells harvested immediately after thawing (day -3)


title: Fibroblast Day+3 +4F Experiment 1

description: Individual sample


title: Adult Fibroblasts Sample 1 DNA Methylome

description: Individual sample

source_name: Adult Fibroblasts Sample 1

value: Adult Fibroblasts Sample 1

value: Provided by R.A. Reijo-Pera (Stanford).


title: Fibroblast Day+3 +4F Experiment 3

description: Individual sample

value: adult fibroblasts


title: hESC (SC233) p29 DNA Methylome

description: Individual sample

source_name: SC233 human Embryonic Stem Cells, Passage 29 (Stemride International, SI-233)


title: CD4+Tcells_24 h_stimulated_control 14

city: Linkoping

first: Daniel

last: Eklund

address: Universitetssjukhuset

country: Sweden

institute: Linkoping University

description:
Ctrl14_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

hyb_protocol: 600 ng of cRNA (specific activity Cy3 > 8 pmol Cy3 per µg cRNA) was hybridized onto Agilent Sureprint G3 Human Gene Expression 8x60k arrays (Agilent Technologies) using the Gene Expression Hybridization Kit (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k G3 array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data extraction and quality control fulfillment was performed with the Feature Extraction software version 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1-107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CD4+ T cells_24 h_stimulated_healthy control

label_protocol: 50 ng of RNA from each sample was amplified and labelled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) and the Cy3-labeled cRNA was purified with RNeasy Mini Kit (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the Allprep DNA/RNA Micro kit (Qiagen) according to the manufacturer´s instructions. The concentration and integrity of the extracted RNA was evaluated using the RNA 6000 Nano Labchip® (Agilent Technologies, Santa Clara, CA, USA) on Agilent 2100 Bioanalyzer (Agilent Technologies). The RNA integrity number ranged from 7.4 to 9.5.

treatment_protocol: Whole blood was collected in sodium-heparin tubes (Vacuette, Greiner Bio-One, Kremsmünster, Austria) from healthy donors (n=14) and patients diagnosed with relapsing-remitting multiple sclerosis (n=14). Peripheral blood mononuclear cells (PBMC) were isolated by density centrifugation (Lymphoprep™, Axis-Shield, Oslo, Norway) and washed in Hank’s Balanced Salt Solution (Life Technologies, Darmstadt, Germany). The PBMC were resuspended in freezing medium consisting of 10% dimethyl sulfoxide (DMSO; Sigma-Aldrich, St. Louis, MO, USA), 50% heat-inactivated fetal bovine serum (FBS Hyclone; Thermo Fisher Scientific, Boston, MA, USA) and 40% Isocove’s Modified Dulbecco’s Medium (IMDM; Invitrogen, Carlsbad, CA, USA) supplemented with L-glutamine (292 mg/l; Sigma-Aldrich), MEM non-essential amino acids 100X (10 ml/l; Gibco®), penicillin (50 IE/ml), streptomycin (50 mg/ml; Cambrex-Lonza, Basel, Switzerland), and sodium bicarbonate (3.024 g/l; Sigma-Aldrich) and aliqouted at a cell density between 4.5-11.5 million PBMC/ml. The cells were placed in a freezing container at -70ºC overnight and subsequently transferred and stored in liquid nitrogen until use. The PBMC were later thawed in a 37°C water bath and washed with IMDM supplemented with 10% FBS (IMDM+10%FBS). CD4+ T cells were isolated by immunomagnetic positive selection according to the instructions provided by the manufacturer using MS columns and a miniMACS separator (Miltenyi Biotec, Bergisch Gladbach, Germany). The purity of the isolated CD4+ T cells was >96%, based on flow cytometry. Isolated CD4+ T cells were cultured unstimulated (resting) or stimulated (activated by anti-CD3/28 antibodies (0.03 µg/ml)) at a density of 2 million cells/ml, in IMDM + 5% FBS, for 24 h at 37°C.

tag: subject id

value: control 14

tag: subject status

value: healthy control

tag: gender

value: female

tag: age (yrs)

tag: tissue

value: isolated CD4+ cells

tag: stimulated with

value: anti-CD3/-CD28  (0.03 µg/ml) for 24hrs


title: hESC (H9) p45 DNA Methylome

description: Individual sample

source_name: H9 human Embryonic Stem Cells, Passage 45 (NIH Code WA09)


title: Cord Blood Day -3, Experiment 3

description: Individual sample


title: hESC (H1) p55 DNA Methylome

description: Individual sample

source_name: H1 human Embryonic Stem Cells, Passage 55 (NIH Code WA01)


title: Fibroblast Day zero, Experiment 2

description: Individual sample

tag: cell line

value: Fibroblasts passaged 2-3 days prior to day 0 and then harvested on day zero


title: CD4+Tcells_24 h_stimulated_control 13

description:
Ctrl13_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: control 13


title: CD4+Tcells_24 h_stimulated_control 12

description:
Ctrl12_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: control 12


title: hESC (ESO3) p87 DNA Methylome

description: Individual sample

source_name: ES03 human Embryonic Stem Cells, Passage 87 (ES Cell International)


title: Fibroblast Day zero, Experiment 1

description: Individual sample


title: CD4+Tcells_24 h_stimulated_control 11

description:
Ctrl11_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: control 11


title: hESC (ESO3) p76 DNA Methylome

description: Individual sample

source_name: ES03 human Embryonic Stem Cells, Passage 76 (ES Cell International)

value: Undifferentiated hESC


title: Cord Blood CD34+ progenitors Sample 3 DNA Methylome

description: Individual sample

source_name: Cord Blood CD34+ progenitors_Day 0

value: Cord Blood CD34+ progenitors_Day 0

value: Obtained from ALLCELLS (Emeryville, CA), stimulated with Flt3L, TPO, SCF X 3 days


title: CD4+Tcells_24 h_stimulated_control 7

description:
Ctrl7_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: control 7


title: CD4+Tcells_24 h_stimulated_control 9

description:
Ctrl9_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: control 9


title: Cord Blood CD34+ progenitors Sample 2 DNA Methylome

description: Individual sample


title: CD4+Tcells_24 h_stimulated_control 6

description:
Ctrl6_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: control 6


title: CD4+Tcells_24 h_stimulated_control 10

description:
Ctrl10_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: control 10


title: hESC (ESO3) p86 DNA Methylome

description: Individual sample

source_name: ES03 human Embryonic Stem Cells, Passage 86 (ES Cell International)


title: DEP treated mouse ear Replicate 3

city: Goyang

first: Hyo-Jeong

last: Kim

address: 32, Dongguk-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do 10326, Republic of Korea

country: South Korea

institute: Dongguk University

description: Biological replicate 3 of 4. DEP treated mouse ear.

hyb_protocol: Labeled cRNA was hybridized on Mouse (V2) Gene Expression Microarray 4x44K (ID G2519-026655; Agilent Technologies) followed by manual washing, according to the manufacturer’s procedures.

scan_protocol: Scanned on an Agilent SureScan microarray scanner.

data_processing: Probe signals were quantified using Feature Extraction software (version 10.10.1.1; Agilent) and data were nomalized using Subio platform v1.16.4376 (Subio Inc. Japan)

organism: Mus musculus

label_protocol: The RNA samples were labeled using a Low Input Quick Amp Labeling Kit (Agilent Technologies), in accordance with the manufacturer’s protocol.

extract_protocol: Total RNA was extracted using an RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s recommendations.

tag: treatment

value: DEP

value: Ear


title: DEP treated mouse ear Replicate 4

description: Biological replicate 4 of 4. DEP treated mouse ear.


title: DEP treated mouse ear Replicate 2

description: Biological replicate 2 of 45. DEP treated mouse ear.


title: viral fibroblast iPSC line IMR90-4 p63 DNA Methylome

description: Individual sample

source_name: viral fibroblast iPSC clone iPS(IMR90)-4 passage 63

value: Obtained from WiCell (Madison, WI). Originally derived in Yu et al. Science 318:1917-1920. 1997.


title: CD4+Tcells_24 h_stimulated_control 5

description:
Ctrl5_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: control 5

value: healthy control

value: female


title: CD4+Tcells_24 h_stimulated_patient 14

description:
MS14_stim
Gene expression in CD4+ T cells from multiple sclerosis patient, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

source_name: CD4+ T cells_24 h_stimulated_MS patient

value: patient 14

value: Multiple Sclerosis (MS) patient

value: isolated CD4+ cells

value: anti-CD3/-CD28  (0.03 µg/ml) for 24hrs


title: CD4+Tcells_24 h_stimulated_control 8

description:
Ctrl8_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: control 8


title: CD4+Tcells_24 h_stimulated_patient 13

description:
MS13_stim
Gene expression in CD4+ T cells from multiple sclerosis patient stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: patient 13


title: CD4+Tcells_24 h_stimulated_control 4

description:
Ctrl4_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: control 4


title: CD4+Tcells_24 h_stimulated_control 1

description:
Ctrl1_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: control 1


title: viral fibroblast iPSC line IMR90-1 p75 DNA Methylome

description: Individual sample

source_name: viral fibroblast iPSC clone iPS(IMR90)-1 passage 75


title: cells with mixture, biological rep2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from human breast cancer cells T47D-KBluc exposed to a mixture of diclofenac (50uM), sulfamethoxazole (50uM) and ofloxacin (50uM)

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of human HG-U133_Plus_2-type from Affymetrix. A Custom CDF Version 14 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: T47D-KBluc cells exposed to a mixture of diclofenac (50uM), sulfamethoxazole (50uM) and ofloxacin (50uM)

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

growth_protocol: Cells were grown in RPMI 1640, supplemented with sodium pyruvate (1%), Fetal Bovine Serum (FBS) (10%) and 50 U/mL mixture of penicillin and streptomycin (1%)

extract_protocol: The NucleoSpin RNA II kit was used for extraction as per manufacturer's  instructions

treatment_protocol: Cells were grown for 24 h in growth medium and then for 40 h in  assay medium (lacking antibiotics) in the presence of the different types of mixtures

tag: concentration

tag: uv-irradiation

value: control


title: DEP treated mouse ear Replicate 1

description: Biological replicate 1 of 4. DEP treated mouse ear.


title: CD4+Tcells_24 h_stimulated_control 3

description:
Ctrl3_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: control 3


title: CD4+Tcells_24 h_stimulated_control 2

description:
Ctrl2_stim
Gene expression in CD4+ T cells from healthy subject, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: control 2


title: nonviral Keratinocyte iPSC clone 1 p14 DNA Methylome

description: Individual sample

source_name: nonviral Keratinocyte iPSC clone 3, passage 14

value: non-integrated keratinocyte iPSC generated in the Zambidis laboratory


title: cells control, biological rep2

description: Gene expression data from human breast cancer cells T47D-KBluc exposed to deionized water

source_name: T47D-KBluc cells exposed to deionized water


title: CD4+Tcells_24 h_stimulated_patient 10

description:
MS10_stim
Gene expression in CD4+ T cells from multiple sclerosis patient stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: patient 10


title: CD4+Tcells_24 h_stimulated_patient 5

description:
MS5_stim
Gene expression in CD4+ T cells from multiple sclerosis patient stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: patient 5


title: CD4+Tcells_24 h_stimulated_patient 12

description:
MS12_stim
Gene expression in CD4+ T cells from multiple sclerosis patient stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: patient 12


title: CD4+Tcells_24 h_stimulated_patient 9

description:
MS9_stim
Gene expression in CD4+ T cells from multiple sclerosis patient stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: patient 9


title: nonviral 4F stromal primed fetal liver iPSC clone 3 p11 DNA Methylome

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) Fetal Liver iPSC clone 3, passage 11

value: non-integrated stromal primed fetal liver iPSC generated in the Zambidis laboratory


title: nonviral 4F stromal primed fetal liver iPSC clone 1 p12 DNA Methylome

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) Fetal Liver iPSC clone 1, passage 12


title: cells with irradiated mixture, biological rep2

description: Gene expression data from human breast cancer cells T47D-KBluc exposed to a mixture of diclofenac (50uM), sulfamethoxazole (50uM) and ofloxacin (50uM) irradiated with UV for 15 min

source_name: T47D-KBluc cells exposed to a mixture of diclofenac (50uM), sulfamethoxazole (50uM) and ofloxacin (50uM) irradiated for 15 min

value: irradiated


title: cells with mixture, biological rep1


title: CD4+Tcells_24 h_stimulated_patient 11

description:
MS11_stim
Gene expression in CD4+ T cells from multiple sclerosis patient stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: patient 11

value: Multiple Sclerosis (MS) patient

value: female


title: CD4+Tcells_24 h_stimulated_patient 1

description:
MS1_stim
Gene expression in CD4+ T cells from multiple sclerosis patient, stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: patient 1

value: isolated CD4+ cells

value: none (unstimulated) for 24hrs


title: nonviral 4F stromal primed fetal liver iPSC clone 6 p11 DNA Methylome

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) Fetal Liver iPSC clone 6, passage 11


title: CD4+Tcells_24 h_stimulated_patient 6

description:
MS6_stim
Gene expression in CD4+ T cells from multiple sclerosis patient stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: patient 6

value: anti-CD3/-CD28  (0.03 µg/ml) for 24hrs


title: Cord Blood CD34+ progenitors Sample 1 DNA Methylome

description: Individual sample

value: Cord Blood CD34+ progenitors_Day 0

value: Obtained from ALLCELLS (Emeryville, CA), stimulated with Flt3L, TPO, SCF X 3 days


title: CD4+Tcells_24 h_stimulated_patient 7

description:
MS7_stim
Gene expression in CD4+ T cells from multiple sclerosis patient stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: patient 7


title: CD4+Tcells_24 h_stimulated_patient 8

description:
MS8_stim
Gene expression in CD4+ T cells from multiple sclerosis patient stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: patient 8


title: cells control, biological rep1

value: control


title: CD4+Tcells_24 h_stimulated_patient 4

description:
MS4_stim
Gene expression in CD4+ T cells from multiple sclerosis patient stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: patient 4


title: nonviral 7F Adult fibroblast iPSC clone 6.6 p12 DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) fetal Fibroblast iPSC clone 6.6, passage 12

value: non-integrated fetal Fibroblast iPSC generated in the Zambidis laboratory


title: nonviral 7F Adult fibroblast iPSC clone 6.1 p12 DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) fetal Fibroblast iPSC clone 6.1, passage 12


title: nonviral 7F Adult fibroblast iPSC clone WT4 p15 DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) Adult Fibroblast iPSC clone WT4, passage 15

value: non-integrated Adult Fibroblast iPSC generated in the Zambidis laboratory


title: nonviral 7F Adult fibroblast iPSC clone WT2 p15 DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) Adult Fibroblast iPSC clone WT2, passage 15


title: cells with irradiated mixture, biological rep1

value: irradiated


title: CD4+Tcells_24 h_unstimulated_control 11

description:
Ctrl11_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

source_name: CD4+ T cells_24 h_unstimulated_healthy control

value: control 11

value: healthy control


title: CD4+Tcells_24 h_unstimulated_control 12

description:
Ctrl12_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

value: control 12

value: female


title: CD4+Tcells_24 h_unstimulated_control 13

description:
Ctrl13_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

value: control 13

value: isolated CD4+ cells


title: CD4+Tcells_24 h_stimulated_patient 2

description:
MS2_stim
Gene expression in CD4+ T cells from multiple sclerosis patient stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: patient 2

value: Multiple Sclerosis (MS) patient


title: CD4+Tcells_24 h_stimulated_patient 3

description:
MS3_stim
Gene expression in CD4+ T cells from multiple sclerosis patient stimulated with 0.03 µg anti-CD3/CD28 antibiodies after 24 h incubation.

value: patient 3

value: anti-CD3/-CD28  (0.03 µg/ml) for 24hrs


title: CD4+Tcells_24 h_unstimulated_control 9

description:
Ctrl9_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

value: control 9

value: none (unstimulated) for 24hrs


title: CD4+Tcells_24 h_unstimulated_control 14

description:
Ctrl14_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

value: control 14


title: CD4+Tcells_24 h_unstimulated_control 10

description:
Ctrl10_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

value: control 10


title: viral 4F Adult Fibroblast iPSC clone HUF5 p15 DNA Methylome

description: Individual sample

source_name: viral 4 factor (SOX2, OCT4, KLF4, cMYC) Adult Fibroblast iPSC clone HUF5, passage 15

value: Provided by R.A. Reijo-Pera (Stanford). Originally derived in Byrne et al. PLOS One 4(9):e7118. (2009)


title: viral 4F Adult Fibroblast iPSC clone HUF17 p10 DNA Methylome

description: Individual sample

source_name: viral 4 factor (SOX2, OCT4, KLF4, cMYC) Adult Fibroblast iPSC clone HUF17, passage 10


title: CD4+Tcells_24 h_unstimulated_control 8

description:
Ctrl8_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

value: control 8


title: CD4+Tcells_24 h_unstimulated_control 7

description:
Ctrl7_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

value: control 7


title: viral 4F Adult Fibroblast iPSC clone HUF1 p11 DNA Methylome

description: Individual sample

source_name: viral 4 factor (SOX2, OCT4, KLF4, cMYC) Adult Fibroblast iPSC clone HUF1, passage 11


title: nonviral 7F Neonatal fibroblast iPSC clone 7ta p44 DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) neonatal Fibroblast iPSC clone 7ta, passage 44

value: Obtained from WiCell (Madison, WI). Originally derived in Yu et al. Science 324:797-801 (2009).


title: CD4+Tcells_24 h_unstimulated_control 4

description:
Ctrl4_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

value: control 4

value: healthy control


title: viral 4F Adult Fibroblast iPSC clone HUF3 p20 DNA Methylome

description: Individual sample

source_name: viral 4 factor (SOX2, OCT4, KLF4, cMYC) Adult Fibroblast iPSC clone HUF3, passage 20


title: CD4+Tcells_24 h_unstimulated_control 3

description:
Ctrl3_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

value: control 3

value: female


title: CD4+Tcells_24 h_unstimulated_control 2

description:
Ctrl2_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

value: control 2

value: isolated CD4+ cells


title: nonviral 7F stromal primed cord blood iPSC clone E2C4 p12 DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone E2C4, passage 12

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory


title: CD4+Tcells_24 h_unstimulated_control 6

description:
Ctrl6_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

value: control 6


title: CD4+Tcells_24 h_unstimulated_control 5

description:
Ctrl5_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

value: control 5


title: CD4+Tcells_24 h_unstimulated_patient 13

description:
MS13_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

source_name: CD4+ T cells_24 h_unstimulated_MS patient

value: patient 13

value: Multiple Sclerosis (MS) patient


title: CD4+Tcells_24 h_unstimulated_patient 14

description:
MS14_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

value: patient 14

value: none (unstimulated) for 24hrs


title: nonviral 4F stromal primed cord blood iPSC clone E5C3 p10 DNA Methylome

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed Cord Blood iPSC clone E5C3, passage 10


title: CD4+Tcells_24 h_unstimulated_patient 10

description:
MS10_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

value: patient 10


title: nonviral 7F stromal primed cord blood iPSC clone E2C3 p12 DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone E2C3, passage 12


title: CD4+Tcells_24 h_unstimulated_patient 12

description:
MS12_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

value: patient 12


title: CD4+Tcells_24 h_unstimulated_patient 9

description:
MS9_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

value: patient 9


title: CD4+Tcells_24 h_unstimulated_control 1

description:
Ctrl1_unstim
Gene expression in untreated CD4+ T cells from healthy subject after 24 h incubation.

value: control 1


title: CD4+Tcells_24 h_unstimulated_patient 5

description:
MS5_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

value: patient 5


title: nonviral 4F stromal primed cord blood iPSC clone E5C4 p9 DNA Methylome

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed Cord Blood iPSC clone E5C4, passage 9


title: CD4+Tcells_24 h_unstimulated_patient 11

description:
MS11_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

value: patient 11


title: CD4+Tcells_24 h_unstimulated_patient 3

description:
MS3_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

value: patient 3


title: CD4+Tcells_24 h_unstimulated_patient 8

description:
MS8_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

value: patient 8

value: female


title: nonviral 7F stromal primed cord blood iPSC clone E2C2 p12 DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone E2C2, passage 12


title: CD4+Tcells_24 h_unstimulated_patient 4

description:
MS4_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

value: patient 4

value: isolated CD4+ cells


title: CD4+Tcells_24 h_unstimulated_patient 7

description:
MS7_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

value: patient 7


title: CD4+Tcells_24 h_unstimulated_patient 1

description:
MS1_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

value: patient 1


title: nonviral 7F stromal primed cord blood iPSC clone E1C3 p12 DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone E1C3, passage 12

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory


title: nonviral 7F stromal primed cord blood iPSC clone E1C4 p12 DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone E1C4, passage 12


title: nonviral 7F stromal primed cord blood iPSC clone 6.2 p21 DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone 6.2, passage 21


title: Male wild type cardiomyocytes 453

city: Winston-Salem

first: Hao

last: Wang

state: NC

address: Medical Center Boulevard

department: Anesthesiology

institute: Wake Forest School of Medicine

hyb_protocol: 10 ug biotinylated cRNA was hybridized to the Affymetrix Gene Atlas Mouse MG-430 PM Array Strips according to current Affymetrix protocols.

scan_protocol: The arrays were washed and scanned according to standard Affymetrix GeneAtlas instructions using the GeneAtlas scanner and software control (GeneAtlas Instrument Control (GAIC) v. 1.0.5.267.).

data_processing: Raw data (CEL files) were generated using Affymetrix AGCC software and quantile normalized by the RMA method. Log intensity distributions, pair-wise correlations and internal Affymetrix controls were examined to evaluate hybridization quality using Partek Genomics Suite software (Partek Inc.).

label: Biotin

source_name: cardiomyocyte

label_protocol: 250 ng total RNA was amplified and labeled according to the Affymetrix 3’-IVT labeling protocol.

extract_protocol: Total RNA was isolated from cardiomyocytes using the RNeasy Lipit Tissue Mini Kit (Qiagen Inc) and further purified using RNeasy MinElute Cleanup Kit (Qiagen Inc)

tag: genotype

value: wild type

value: cardiomyocyte

tag: age

value: 15 weeks

value: Male


title: nonviral 4F stromal primed cord blood iPSC clone E5C1 p9 DNA Methylome

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed Cord Blood iPSC clone E5C1, passage 9

tag: cell type

tag: sample type


title: Male wild type cardiomyocytes 452


title: nonviral 7F stromal primed cord blood iPSC clone E1C2 p12 DNA Methylome

description: Individual sample

value: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone E1C3, passage 12


title: CD4+Tcells_24 h_unstimulated_patient 2

description:
MS2_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

value: patient 2

value: Multiple Sclerosis (MS) patient

value: none (unstimulated) for 24hrs


title: nonviral 7F stromal primed cord blood iPSC clone 6.2, unknown passage,  DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone 6.2, unknown passage

value: unknown

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory; because of unknown passage, this sample was not included in methylation analyses in Park et al. 2012


title: Male GPER-knockout cardiomyocytes 451

value: GPER-knockout


title: nonviral 7F stromal primed cord blood iPSC clone 6.11 p14 DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone 6.11, passage 14


title: Male GPER-knockout cardiomyocytes 432


title: Male GPER-knockout cardiomyocytes 431


title: Male wild type cardiomyocytes 433


title: Female GPER-knockout cardiomyocytes 426

value: Female


title: Female wild type cardiomyocytes 425


title: Male GPER-knockout cardiomyocytes 444


title: Female wild type cardiomyocytes 421


title: nonviral 7F stromal primed cord blood iPSC clone 19.11 p14 DNA Methylome

description: Individual sample

source_name: nonviral 7F stromal primed cord blood iPSC clone 19.11 passage 14


title: nonviral 7F stromal primed cord blood iPSC clone 6.13 p14 DNA Methylome

description: Individual sample

source_name: nonviral 7F stromal primed cord blood iPSC clone 6.13 passage 22


title: Female wild type cardiomyocytes 422


title: Male wild type cardiomyocytes 430


title: Female GPER-knockout cardiomyocytes 427


title: Female wild type cardiomyocytes 418


title: Female GPER-knockout cardiomyocytes 419


title: Female GPER-knockout cardiomyocytes 417


title: L591 cells transfected with pcDNA3-PDLIM2 transcript variant 2 (tv 2)  and pEGFP-N3 2

city: Berlin

first: Stephan

last: Mathas

address: Robert-Rössle-Straße 10

institute: MDC Berlin

description: Hodgkin Lymphoma cell line

hyb_protocol: According to Illumina proprietary protocol.

data_processing: Raw microarray data were background corrected with Illumina’s proprietary background correction routine and quantile normalization were applied. Subsequently, data were log2 transformed.

molecule: polyA RNA

source_name: L591 cells

growth_protocol: As described in Lamprecht B, Bonifer C, Mathas S. Repeat-element driven activation of proto-oncogenes in human malignancies. Cell Cycle 2010; 9: 4276–4281.

treatment_protocol: L591 cells were transfected with 40 μg of a pcDNA3-PDLIM2 transcript variant 2 (tv 2)  or mock pcDNA3 construct along with 10 μg pEGFP-N3. GFP+ cells were enriched by fluorescence-activated cell sorting.

tag: transfection


title: L591 cells transfected with mock pcDNA3 and pEGFP-N3 2

description: Hodgkin Lymphoma cell line

scan_protocol: According to Illumina proprietary protocol.

extract_protocol: As described in Lamprecht B, Bonifer C, Mathas S. Repeat-element driven activation of proto-oncogenes in human malignancies. Cell Cycle 2010; 9: 4276–4281.

value: mock pcDNA3 and pEGFP-N3


title: L591 cells transfected with pcDNA3-PDLIM2 transcript variant 2 (tv 2)  and pEGFP-N3 1

description: Hodgkin Lymphoma cell line

label_protocol: According to Illumina proprietary protocol.


title: L591 cells transfected with mock pcDNA3 and pEGFP-N3 1

description: Hodgkin Lymphoma cell line


title: nonviral 4 factor stromal primed cord blood iPSC clone LZ6+2, passage 19

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone LZ6+2, passage 19


title: gastric cancer plasmas 850

city: Guangzhou

first: Yejia

last: Cui

address: NO1 Panfu Road

country: China

institute: Guangzhou First People's Hospital

description: Gene expression

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

scan_protocol: Following the washing steps the slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: gastric cancer plasmas

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

tag: diagnosis

value: gastric cancer

value: male

tag: tmn stage

value: I


title: gastric cancer plasmas 843

description: Gene expression

value: female

value: III


title: nonviral 4 factor stromal primed Cord Blood iPSC clone E5C1, passage 32

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed Cord Blood iPSC clone E5C1, passage 32

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory


title: nonviral 7 factor  Adult Fibroblast iPSC clone 7F-C1.2, passage 13

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) Adult Fibroblast iPSC clone 7F-C1.2, passage 13

value: non-integrated Adult Fibroblast iPSC generated in the Zambidis laboratory


title: nonviral 4 factor stromal primed cord blood iPSC clone E17C6 passage 14

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E17C6 passage 14


title: CD4+Tcells_24 h_unstimulated_patient 6

description:
MS6_unstim
Gene expression in untreated CD4+ T cells from multiple sclerosis patient after 24 h incubation.

source_name: CD4+ T cells_24 h_unstimulated_MS patient

tag: subject id

value: patient 6

value: isolated CD4+ cells


title: health control plasmas 4

description: Gene expression

source_name: health control plasmas

value: healthy


title: gastric cancer plasmas 594

description: Gene expression

value: IV


title: nonviral 7F stromal primed cord blood iPSC clone E1C11 p12 DNA Methylome

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone E1C11, passage 12

tag: passage


title: nonviral 7 factor  Adult Fibroblast iPSC clone 7F-C2, passage 13

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) Adult Fibroblast iPSC clone 7F-C2, passage 13


title: nonviral 4 factor stromal primed cord blood iPSC clone LZ6+10, passage 13

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone LZ6+10, passage 13


title: nonviral 7F stromal primed cord blood iPSC clone 6.2 p18

description: Individual sample

source_name: nonviral 7F  (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed cord blood iPSC clone 6.2 passage 15

value: nonviral 7F stromal primed cord blood iPSC clone 6.2 passage 15


title: nonviral 4 factor stromal primed cord blood iPSC clone LZ6+2, passage 17, p4 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone LZ6+2, passage 17, p4 after conversion to a naïve state with L3i

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory, p4 after conversion to a naïve state with L3i


title: nonviral 7F fetal fibroblast iPSC clone 6.1 p23

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) fetal Fibroblast iPSC clone 6.1, passage 23

value: non-integrated fetal Fibroblast iPSC generated in the Zambidis laboratory


title: Control _vs_growth hormone-treated  3T3-F442A adipocytes

city: Jinan

first: Yuchao

last: Zhang

address: 44 Wenhua Road West

institute: Shandong University

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Arrays were scanned with a confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

source_name: 3T3 cell line_control

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, 2 and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: The mouse embryo ﬁbroblasts 3T3-F442A were cultured and induced to differentiate, at 12 days approximately 80% 80% 3T3-F442A cells were differentiated into adipocytes. And then cultures with DMEM containing 10% FBS every other day.

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

treatment_protocol: The differentiated 3T3-F442A cells were treated with GH for 24 H (at final concentration of 125 ng/mL).

value: adipocytes

source_name: 3T3 cell line_growth hormone-treated


title: gastric cancer plasmas 682

description: Gene expression

tag: gender


title: gastric cancer plasmas 623

description: Gene expression

value: II


title: nonviral 4 factor stromal primed cord blood iPSC clone E5C3 passage 18

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E5C3 passage 18


title: nonviral 4 factor stromal primed cord blood iPSC clone E17C6 passage 27, p4 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E17C6 passage 27, p4 after conversion to a naïve state with L3i


title: hESC (ESO3) p87, p7 after conversion to a naïve state with L3i

description: Individual sample

source_name: ES03 human Embryonic Stem Cells, Passage 87 (ES Cell International), p7 after conversion to a naïve state with L3i

value: Undifferentiated hESC, p7 after conversion to a naïve state with L3i


title: nonviral 7 factor  Adult Fibroblast iPSC clone 7F-C2, passage 9, p4 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) Adult Fibroblast iPSC clone 7F-C2, passage 9, p4 after conversion to a naïve state with L3i

value: non-integrated Adult Fibroblast iPSC generated in the Zambidis laboratory, p4 after conversion to a naïve state with L3i


title: nonviral 4 factor stromal primed Cord Blood iPSC clone E5C1, passage 27, p4 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed Cord Blood iPSC clone E5C1, passage 27, p4 after conversion to a naïve state with L3i


title: hESC (ESO3) p

description: Individual sample

source_name: ES03 human Embryonic Stem Cells, Passage 88 (ES Cell International)

value: Undifferentiated hESC


title: hESC (H9) p38

description: Individual sample

source_name: H9 human Embryonic Stem Cells, Passage 38 (NIH Code WA09)


title: nonviral 7F fetal fibroblast iPSC clone 6.1, passage 38, p7 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) fetal Fibroblast iPSC clone 6.1, passage 38, p7 after conversion to a naïve state with L3i

value: non-integrated fetal Fibroblast iPSC generated in the Zambidis laboratory p7 after conversion to a naïve state with L3i


title: nonviral 7F  stromal primed cord blood iPSC clone 6.2 passage 26, p7 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 7F  (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed cord blood iPSC clone 6.2 passage 26, p7 after conversion to a naïve state with L3i

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory, p7 after conversion to a naïve state with L3i


title: hESC (H7) p42, P6 after conversion to a naïve state with L3i

description: Individual sample

source_name: H7 human Embryonic Stem Cells, Passage 42 (NIH Code WA07), P6 after conversion to a naïve state with L3i

value: Undifferentiated hESC, P6 after conversion to a naïve state with L3i


title: nonviral 7 factor  Adult Fibroblast iPSC clone 7F-C1.2, passage 9, p4 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) Adult Fibroblast iPSC clone 7F-C1.2, passage 9, p4 after conversion to a naïve state with L3i


title: hESC (H7) p46

description: Individual sample

source_name: H7 human Embryonic Stem Cells, Passage 46 (NIH Code WA07)


title: hESC (H9) p34, P4 after conversion to a naïve state with L3i

description: Individual sample

source_name: H9 human Embryonic Stem Cells, Passage 34 (NIH Code WA09), P4 after conversion to a naïve state with L3i

value: Undifferentiated hESC, P4 after conversion to a naïve state with L3i


title: nonviral 4 factor stromal primed cord blood iPSC clone E5C3 passage 22, p5 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone E5C3 passage 22, p5 after conversion to a naïve state with L3i

value: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory, p5 after conversion to a naïve state with L3i


title: nonviral 4 factor stromal primed cord blood iPSC clone LZ6+10 passage 17, p4 after conversion to a naïve state with L3i

description: Individual sample

source_name: nonviral 4 factor (SOX2, OCT4, KLF4, MYC) stromal primed cord blood iPSC clone LZ6+10, passage 17, p4 after conversion to a naïve state with L3i


title: health control plasmas 1

description: Gene expression

source_name: health control plasmas

value: male


title: CD4+ CD44hiCD62LloChAT-eGFP−, replicate 3

status: Public on Sep 12 2016

city: Manhasset

first: Peder

last: Olofsson

address: 350 Community Drive

institute: Feinstein Institute

hyb_protocol: According to a modified ImmGen protocol (http://www.immgen.org, https://www.immgen.org/Protocols/ImmGen%20Cell%20prep%20and%20sorting%20SOP.pdf). Subsequent RNA isolation and Affymetrix Mouse ST 1.0 gene array hybridization experiments were performed by ImmGen.

data_processing:
Data analysis was performed using the R programming language. The R/Bioconductor package “oligo” was used for data import and normalization (through ‘rma’) and the packages “pd.mogene.1.0.st.v1”, “mogene10sttranscriptcluster.db”, and the getNetAffx function from the “oligo” package for annotation of transcripts.
Data were normalized with rma from R/Bioconductor package oligo. Transcript level values are used for analysis.

source_name: spleen

extract_protocol: ChAT-eGFP+ and ChAT-eGFP− cells were isolated from spleens of B6.Cg-Tg(RP23-268L19-eGFP)2Mik/J reporter mice by negative selection for CD4+ T cells followed by cell sorting by flow cytometry of the CD4 +CD44hiCD62Llo population into eGFP + and eGFP− subsets1. For cell sorting experiments, an enriched CD4+ T-cell suspension was obtained by negative selection (CD4+ T-cell isolation kit II, Miltenyi) of spleen cells harvested from male ChAT(BAC)-eGFP mice. The resulting enriched CD4 + cell suspension with >90% purity was then stained with anti- CD44 PE (eBioscience, 12-0441-81), anti-CD4 Pacific Orange (Invitrogen, MCD0430), anti-CD62L PE-Cy7 (eBioscience, 25-0621-82), and anti-CD19 APC (BD Biosciences, BDB550992) antibodies and 7-AAD solution. After gating out CD19+ and gating for CD62Llo CD44 hi cells, a ChAT-eGFP− and a ChAT-eGFP+ fraction were collected using a FACSAria cell sorter (Becton Dickinson). The resulting fractions were CD4+ CD44hiCD62LloChAT-eGFP− and CD4+CD44hiCD62LloChAT-eGFP +. 100–150,000 cells were sorted into FCS-containing cell culture medium. To improve purity, the freshly sorted cells were immediately sorted again using the same gating strategy, now directly into Trizol solution (Ambion) according to a modified ImmGen protocol (http://www.immgen.org/, https://www.immgen.org/Protocols/ImmGen%20Cell%20prep%20and%20sorting%20SOP.pdf) and subsequently frozen at −80 °C. Subsequent RNA isolation and Affymetrix Mouse ST 1.0 gene array hybridization experiments were performed by ImmGen.

value: spleen

value: negative

tag: cell markers

value: CD4+ CD44hiCD62LloChAT-eGFP−


title: CD4+ CD44hiCD62LloChAT-eGFP+, replicate 2

scan_protocol: According to a modified ImmGen protocol (http://www.immgen.org, https://www.immgen.org/Protocols/ImmGen%20Cell%20prep%20and%20sorting%20SOP.pdf). Subsequent RNA isolation and Affymetrix Mouse ST 1.0 gene array hybridization experiments were performed by ImmGen.

tag: tissue

value: positive

value: CD4+ CD44hiCD62LloChAT-eGFP+


title: CD4+ CD44hiCD62LloChAT-eGFP−, replicate 2

label_protocol: According to a modified ImmGen protocol (http://www.immgen.org, https://www.immgen.org/Protocols/ImmGen%20Cell%20prep%20and%20sorting%20SOP.pdf). Subsequent RNA isolation and Affymetrix Mouse ST 1.0 gene array hybridization experiments were performed by ImmGen.


title: CD4+ CD44hiCD62LloChAT-eGFP+, replicate 3


title: 005MSXH [III], biological rep7

city: Kanagawa

first: Asuka

last: Kamei

address: LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi

department: Project for development of food functionality assessment methods

country: Japan

institute: Kanagawa Academy of Science and technology

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using the Factor Analysis for Robust Microarray Summarization (qFARMS).

source_name: mice fed high fat diet with 0.05% maple syrup extract high for 4 weeks

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (GeneChip® 3' IVT Express kit, Affymetrix).

growth_protocol: Male C57BL/6J mice aged 3 weeks were purchased from Charles River Japan (Kanagawa, Japan) and housed in a room maintained at 21 ± 1°C and 50 ± 10% relative humidity with a 12-h light/dark cycle (light 08:00–20:00; dark 20:00–08:00). Mice were preliminary fed a low-fat diet (LFD) which contained fat at 10 kcal% for acclimation.  After a week of acclimation, mice were divided four groups (n=10 each) and fed for 4 weeks on diet which contained fat at 45 kcal% as high-fat diet (HFD), 45 kcal% plus 0.02% MSXH (002MSXH), 45 kcal% plus 0.05% MSXH (005MSXH), and LFD .  Mice were given a diet and water for 24 h ad libitum. On day 30th after 16 h fasted, animals were euthanized under anesthesia to excise the livers and to collect the blood.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Livers were excised and stored at -80˚C

tag: strain

value: liver

value: eight-week-old


title: 005MSXH [III], biological rep10


title: 005MSXH [III], biological rep4


title: health control plasmas 2

description: Gene expression

value: healthy


title: CD4+ CD44hiCD62LloChAT-eGFP−, replicate 1


title: 005MSXH [III], biological rep8


title: 005MSXH [III], biological rep9


title: 005MSXH [III], biological rep5


title: s_20047_v4

city: Palo Alto

first: Jorg

last: Goronzy

state: CA

address: Rm E4201, Bldg100, 3801 Miranda Ave

department: Medicine

institute: Stanford University

description: sorted CD4 T cells that express CD38 and HLADR, Donor47, day 14 after vericella zoster vaccination

hyb_protocol: standard Agilent hybridyzation protocol

scan_protocol: standard Agilent scan protocol

data_processing: The data were normalised using quantile normalisation with Genespring software

source_name: Donor 47, day14

label_protocol: standard Agilent label protocol

extract_protocol: RNA was prepared using the_versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: M

value: whole blood

value: CD4 T cells


title: s_20040_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor40, day 14 after vericella zoster vaccination

source_name: Donor 40, day14


title: 005MSXH [III], biological rep6


title: 005MSXH [III], biological rep3


title: 005MSXH [III], biological rep2


title: high fat diet [III], biological rep10

source_name: mice fed high fat diet for 4 weeks


title: s_20047_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor47, day 8 after vericella zoster vaccination

source_name: Donor 47, day8


title: high fat diet [III], biological rep8


title: s_20047_v1

description: sorted CD4 T cells that express CD38 and HLADR, Donor47, day 0 of vericella zoster vaccination

source_name: Donor 47, day0


title: 005MSXH [III], biological rep1


title: s_20046_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor46, day 14 after vericella zoster vaccination

source_name: Donor 46, day14

value: F


title: high fat diet [III], biological rep9


title: s_20046_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor46, day 8 after vericella zoster vaccination

source_name: Donor 46, day8


title: Guthrie T-82

city: Darlinghurst

first: Ruth

last: Pidsley

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: infant blood from archival Guthrie cards

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

scan_protocol: Standard Illumina Protocol

data_processing: Raw IDAT files were processed with Illumina’s GenomeStudio software V2011.1 and background normalized using negative control probes to generate methylation β-values which were used for all downstream analyses.

label: Cy5 and Cy3

source_name: Guthrie card blood

label_protocol: Standard Illumina Protocol

growth_protocol: LNCaP prostate cancer cells were cultured as described in PMID 11850822. Normal prostate epithelial cells (PrEC) were cultured according to the manufacturer’s instructions in prostate epithelial growth medium (PrEGM, catalogue no. CC-3166; Cambrex Bio Science) as described in PMID 20173741. Patient-matched cancer associated fibroblasts (CAFs) and non-malignant tissue associated fibroblasts (NAFs) (n=3 pairs) were isolated and validated as described in PMID 23558784

extract_protocol: Genomic DNA for LNCaP and PrEC cell lines was extracted using QIAamp DNA Mini and Blood Mini kit following the manufacturer’s protocol for cultured cells (Qiagen). Genomic DNA was extracted from the CAF and NAF samples using the DNeasy kit (Qiagen) with on-column RNase A digestion. Genomic DNA was extracted from the Guthrie cards using GenSolve technology (IntegenX) followed by purification using the QIAamp DNA micro kit (Qiagen) and an additional ethanol precipitation step.

value: infant blood


title: high fat diet [III], biological rep7


title: s_20040_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor40, day 8 after vericella zoster vaccination

source_name: Donor 40, day8


title: s_20041_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor41, day 14 after vericella zoster vaccination

source_name: Donor 41, day14


title: high fat diet [III], biological rep5


title: high fat diet [III], biological rep4


title: Guthrie T-76


title: s_20041_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor41, day 8 after vericella zoster vaccination

source_name: Donor 41, day8


title: s_20019_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor19, day 14 after vericella zoster vaccination

source_name: Donor 19, day14


title: CD4+ CD44hiCD62LloChAT-eGFP+, replicate 1


title: s_20019_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor19, day 8 after vericella zoster vaccination

source_name: Donor 19, day8


title: s_20019_v1

description: sorted CD4 T cells that express CD38 and HLADR, Donor19, day 0 of vericella zoster vaccination

source_name: Donor 19, day0


title: high fat diet [III], biological rep6


title: CAF A

description: cancer associated fibroblast

source_name: CAF

value: cancer associated fibroblasts (CAF)


title: s_20042_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor42, day 14 after vericella zoster vaccination

source_name: Donor 42, day14


title: high fat diet [III], biological rep3


title: s_20042_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor42, day 8 after vericella zoster vaccination

source_name: Donor 42, day8


title: high fat diet [III], biological rep2


title: Guthrie T-80


title: s_20038_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor38, day 8 after vericella zoster vaccination

source_name: Donor 38, day8


title: s_20039_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor39, day 14 after vericella zoster vaccination

source_name: Donor 39, day14


title: high fat diet [III], biological rep1

source_name: mice fed high fat diet for 4 weeks


title: s_20039_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor39, day 8 after vericella zoster vaccination

source_name: Donor 39, day8


title: 002MSXH [II], biological rep10

source_name: mice fed high fat diet with 0.02% maple syrup extract high for 4 weeks


title: s_20042_v1

description: sorted CD4 T cells that express CD38 and HLADR, Donor42, day 0 of vericella zoster vaccination

source_name: Donor 42, day0


title: s_20039_v1

description: sorted CD4 T cells that express CD38 and HLADR, Donor39, day 0 of vericella zoster vaccination

source_name: Donor 39, day0


title: CAF C

description: cancer associated fibroblast


title: s_20037_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor37, day 14 after vericella zoster vaccination

source_name: Donor 37, day14


title: s_20037_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor37, day 8 after vericella zoster vaccination

source_name: Donor 37, day8


title: 002MSXH [II], biological rep8


title: s_20038_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor38, day 14 after vericella zoster vaccination

source_name: Donor 38, day14


title: 002MSXH [II], biological rep7


title: s_20038_v1

description: sorted CD4 T cells that express CD38 and HLADR, Donor38, day 0 of vericella zoster vaccination

source_name: Donor 38, day0


title: CAF B

description: cancer associated fibroblast


title: 002MSXH [II], biological rep6


title: s_20036_v1

description: sorted CD4 T cells that express CD38 and HLADR, Donor36, day 0 of vericella zoster vaccination

source_name: Donor 36, day0


title: 002MSXH [II], biological rep5


title: high fat diet [II], biological rep8


title: PrEC Rep1

description: primary cell culture of prostate epithelial cells

source_name: PrEC cells

value: primary prostate epithelial cells (PrEC)


title: 002MSXH [II], biological rep3


title: 002MSXH [II], biological rep1


title: Guthrie T-73

description: infant blood from archival Guthrie cards

source_name: Guthrie card blood


title: 002MSXH [II], biological rep9


title: 002MSXH [II], biological rep4


title: high fat diet [II], biological rep7


title: high fat diet [II], biological rep9


title: 002MSXH [II], biological rep2


title: high fat diet [II], biological rep10


title: s_20035_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor35, day 14 after vericella zoster vaccination

source_name: Donor 35, day14


title: LNCaP Rep1

description: transformed prostate cancer cell line

source_name: LNCaP cells

value: prostate cancer cell line (LNCaP)


title: s_20035_v1

description: sorted CD4 T cells that express CD38 and HLADR, Donor35, day 0 of vericella zoster vaccination

source_name: Donor 35, day0


title: s_20034_v1

description: sorted CD4 T cells that express CD38 and HLADR, Donor34, day 0 of vericella zoster vaccination

source_name: Donor 34, day0


title: NAF C

source_name: NAF

value: non-malignant tissue associated fibroblasts (NAF)


title: s_20033_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor33, day 14 after vericella zoster vaccination

source_name: Donor 33, day14


title: s_20035_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor35, day 8 after vericella zoster vaccination

source_name: Donor 35, day8


title: Guthrie T-75


title: s_20036_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor36, day 8 after vericella zoster vaccination

source_name: Donor 36, day8


title: s_20033_v1

description: sorted CD4 T cells that express CD38 and HLADR, Donor33, day 0 of vericella zoster vaccination

source_name: Donor 33, day0


title: s_20034_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor34, day 14 after vericella zoster vaccination

source_name: Donor 34, day14


title: s_20032_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor32, day 14 after vericella zoster vaccination

source_name: Donor 32, day14


title: NAF A

description: non-malignant tissue associated fibroblast


title: s_20032_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor32, day 8 after vericella zoster vaccination

source_name: Donor 32, day8


title: s_20034_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor34, day 8 after vericella zoster vaccination

source_name: Donor 34, day8


title: s_20032_v1

description: sorted CD4 T cells that express CD38 and HLADR, Donor32, day 0 of vericella zoster vaccination

source_name: Donor 32, day0


title: s_20031_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor31, day 14 after vericella zoster vaccination

source_name: Donor 31, day14


title: s_20033_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor33, day 8 after vericella zoster vaccination

source_name: Donor 33, day8


title: s_20036_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor36, day 14 after vericella zoster vaccination

source_name: Donor 36, day14


title: s_20031_v1

description: sorted CD4 T cells that express CD38 and HLADR, Donor31, day 0 of vericella zoster vaccination

source_name: Donor 31, day0


title: s_20023_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor23, day 14 after vericella zoster vaccination

source_name: Donor 23, day14


title: s_20031_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor31, day 8 after vericella zoster vaccination

source_name: Donor 31, day8


title: high fat diet [II], biological rep2

source_name: mice fed high fat diet for 4 weeks

value: male


title: high fat diet [I], biological rep9


title: high fat diet [II], biological rep3


title: high fat diet [I], biological rep8


title: high fat diet [II], biological rep4


title: high fat diet [I], biological rep6


title: high fat diet [I], biological rep5


title: high fat diet [II], biological rep1


title: s_20023_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor23, day 8 after vericella zoster vaccination

source_name: Donor 23, day8


title: high fat diet [I], biological rep7


title: high fat diet [II], biological rep5


title: high fat diet [I], biological rep10


title: s_20023_v1

description: sorted CD4 T cells that express CD38 and HLADR, Donor23, day 0 of vericella zoster vaccination

source_name: Donor 23, day0


title: s_20022_v4

description: sorted CD4 T cells that express CD38 and HLADR, Donor22, day 14 after vericella zoster vaccination

source_name: Donor 22, day14


title: high fat diet [I], biological rep4


title: s_20022_v3

description: sorted CD4 T cells that express CD38 and HLADR, Donor22, day 8 after vericella zoster vaccination

source_name: Donor 22, day8


title: high fat diet [I], biological rep3


title: s_20022_v1

description: sorted CD4 T cells that express CD38 and HLADR, Donor22, day 0 of vericella zoster vaccination

source_name: Donor 22, day0


title: low fat diet [I], biological rep10

source_name: mice fed low fat diet for 4 weeks


title: high fat diet [I], biological rep1


title: low fat diet [I], biological rep9


title: low fat diet [I], biological rep8


title: low fat diet [I], biological rep5


title: high fat diet [I], biological rep2


title: low fat diet [I], biological rep7


title: low fat diet [I], biological rep2


title: low fat diet [I], biological rep4


title: low fat diet [I], biological rep1


title: 20035-V1

description:
This is twin sibling of Donor 36
Donor 35 day 0 after vericella zoster vaccination

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with Genespring software

source_name: Donor 35 day 0

label_protocol: Standard Illumina label protocol

extract_protocol: total RNA extraction


title: 20019-V2

description: Donor 19 day 1 after vericella zoster vaccination

source_name: Donor 19 day 1


title: low fat diet [I], biological rep3


title: 20019-V1

description: Donor 19 day 0 after vericella zoster vaccination

source_name: Donor 19 day 0


title: 20031-V2

description:
This is twin sibling of Donor 32
Donor 31 day 1 after vericella zoster vaccination

source_name: Donor 31 day 1


title: 20031-V1

description: Donor 31 day 0 after vericella zoster vaccination

source_name: Donor 31 day 0


title: 20036-V2

description: Donor 36 day 1 after vericella zoster vaccination

source_name: Donor 36 day 1


title: 20034-V1

description: Donor 34 day 0 after vericella zoster vaccination

source_name: Donor 34 day 0


title: 20033-V2

description:
This is twin sibling of Donor 34
Donor 33 day 1 after vericella zoster vaccination

source_name: Donor 33 day 1


title: 20035-V2

description: Donor 35 day 1 after vericella zoster vaccination

source_name: Donor 35 day 1


title: low fat diet [I], biological rep6


title: 20020-V2

description: Donor 20 day 1 after vericella zoster vaccination

source_name: Donor 20 day 1


title: 20036-V1

description:
This is twin sibling of Donor 35
Donor 36 day 0 after vericella zoster vaccination

source_name: Donor 36 day 0


title: 20023-V2

description: Donor 23 day 1 after vericella zoster vaccination

source_name: Donor 23 day 1


title: 20020-V1

description: Donor 20 day 0 after vericella zoster vaccination

source_name: Donor 20 day 0


title: 20034-V2

description:
This is twin sibling of Donor 33
Donor 34 day 1 after vericella zoster vaccination

source_name: Donor 34 day 1


title: 20023-V1

description: Donor 23 day 0 after vericella zoster vaccination

source_name: Donor 23 day 0


title: 20032-V2

description:
This is twin sibling of Donor 31
Donor 32 day 1 after vericella zoster vaccination

source_name: Donor 32 day 1


title: 20033-V1

description: Donor 33 day 0 after vericella zoster vaccination

source_name: Donor 33 day 0


title: 20032-V1

description: Donor 32 day 0 after vericella zoster vaccination

source_name: Donor 32 day 0


title: 20043-V1

description: Donor 43 day 0 after vericella zoster vaccination

source_name: Donor 43 day 0


title: 20041-V1

description: Donor 41 day 0 after vericella zoster vaccination

source_name: Donor 41 day 0


title: 20047-V2

description: Donor 47 day 1 after vericella zoster vaccination

source_name: Donor 47 day 1


title: 20047-V1

description: Donor 47 day 0 after vericella zoster vaccination

source_name: Donor 47 day 0


title: 20041-V2

description:
This is twin sibling of Donor 42
Donor 41 day 1 after vericella zoster vaccination

source_name: Donor 41 day 1


title: 20037-V2

description: Donor 37 day 1 after vericella zoster vaccination

source_name: Donor 37 day 1


title: 20043-V2

description: Donor 43 day 1 after vericella zoster vaccination

source_name: Donor 43 day 1


title: 20037-V1

description:
This is twin sibling of Donor 46
Donor 37 day 0 after vericella zoster vaccination

source_name: Donor 37 day 0


title: NAF B

description: non-malignant tissue associated fibroblast

source_name: NAF


title: 20040-V1

description:
This is twin sibling of Donor 38
Donor 40 day 0 after vericella zoster vaccination

source_name: Donor 40 day 0


title: 20040-V2

description: Donor 40 day 1 after vericella zoster vaccination

source_name: Donor 40 day 1


title: 20038-V1

description: Donor 38 day 0 after vericella zoster vaccination

source_name: Donor 38 day 0


title: 20038-V2

description:
This is twin sibling of Donor 40
Donor 38 day 1 after vericella zoster vaccination

source_name: Donor 38 day 1


title: 20039-V2

description: Donor 39 day 1 after vericella zoster vaccination

source_name: Donor 39 day 1


title: high fat diet [II], biological rep6

source_name: mice fed high fat diet for 4 weeks


title: 20046-V2

description: Donor 46 day 1 after vericella zoster vaccination

source_name: Donor 46 day 1


title: 20042-V1

description: Donor 42 day 0 after vericella zoster vaccination

source_name: Donor 42 day 0


title: 20042-V2

description:
This is twin sibling of Donor 41
Donor 42 day 1 after vericella zoster vaccination

source_name: Donor 42 day 1