title: 549559A09 - GRWSB_1 vs GRWWA_1

hyb_protocol: GRWWA_1 Cy5 / GRWSB_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Human male embryo 1

status: Public on Apr 05 2017

type: genomic

city: México

first: Esther

last: Lopez-Bayghen

address: Av. IPN 2508 San Pedro Zac

department: Toxicología

country: Mexico

institute: Cinvestav-IPN

description:
71313-7
Biological replicate 1 of 11. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as male.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)

hyb_protocol: Samples were dissolved in hybridization mix at 75°C for 10 minutes, and incubated overnight at 47°C on the arrays in closed incubation chambers with 50% formamide. The slides were washed 10min in 2xSSC/0.05% Tween20, 10 min 1xSSC, 5min 0.1%SSC at 60°C and 1min in 0.1%SSC at RT

scan_protocol: Scanned on an Innopsys InnoScan 710 laser scan.

data_processing: Images were imported as .tiff and analyzed using BlueFuse Multi 4.3(25799) Software.

molecule: genomic DNA

organism: Homo sapiens

source_name: Trophectoderm human embryo cells

label_protocol: Labelling was done following standard 24sure v3 protocol. In brief, samples were mixed with 5µl of random primers and denaturated for 5min at 94°C. Afterwards, samples were mixed with 12µl of Cy3/Cy5 labelling master mix and incubated at 37°C for 4 hours.

extract_protocol: Whole Genome Amplification performed with Sureplex following manufacturer's instructions.

tag: cell type

value: Human embryo trophectoderm cells biopsied at day 5 by conventional method

source_name: Human reference DNA

tag: sample type

value: SureRef reference DNA


title: Human female embryo 2

description:
72884-10
Biological replicate 2 of 10. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as female.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: 549559A06 - GRWWA_3 vs GRWWB_3

type: RNA

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: What is the effect of a moderate water stress on seed filling (reserve accumulation) and nitrogen remobilisation in pea (Pisum sativum)

hyb_protocol: GRWWB_3 Cy5 / GRWWA_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

molecule: total RNA

organism: Lathyrus oleraceus

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seed - Growth conditions (1-2-3-4):           1  Media   perlite:sand (vol:vol 3:1)  hygrometry   50%  Temperature   15°C night ; 18°C day  Light   16h photoperiod

treatment_protocol: Name:GRWW - environmental treatment - abiotic stress,water-holding capacity of the substrate:quantity 100percent . Pea seeds were sown in 2L pots filled with a mixture (3:1, vol/vol) of perlite and sand and were inocculated with Rhizobium. Watering with a nutritve solution without nitrate (to allow nodulation) was unlimited (drainage conditions) until flowering. At flowering, plants were weighted three times a day in order to maintain a soil relative water content correspondong to the maximum (100%) water holding capacity of the substrate for all the plants. Twelve days after flowering irrigation was stopped for half of the plants (WS plants) until soil water relative content reached 50% of the maximum water-holding capaciy of the substrate. Once this target value was reached (24 hours), it was kept to 50% until samples harvest.

value: Pisum sativum L  - harvest date:03-02-14

value: Pisum sativum L  - harvest date:27-01-14


title: 559665A08 - GRWWB_2 vs GRWSB_2

hyb_protocol: GRWSB_2 Cy5 / GRWWB_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:GRWS - environmental treatment - abiotic stress,water-holding capacity of the substrate:quantity 50percent . Pea seeds were sown in 2L pots filled with a mixture (3:1, vol/vol) of perlite and sand and were inocculated with Rhizobium. Watering with a nutritve solution without nitrate (to allow nodulation) was unlimited (drainage conditions) until flowering. At flowering, plants were weighted three times a day in order to maintain a soil relative water content correspondong to the maximum (100%) water holding capacity of the substrate for all the plants. Twelve days after flowering irrigation was stopped for half of the plants (WS plants) until soil water relative content reached 50% of the maximum water-holding capaciy of the substrate. Once this target value was reached (24 hours), it was kept to 50% until samples harvest.


title: Human female embryo 4

description:
64493-2
Biological replicate 4 of 10. WGA from biopsied cells obtained from day 5 human embryos, classified by PCR as female.
Sample assayed against both female and male references ('combined' file represents combined result of both tests)


title: 549559A01 - GRWWB_1 vs GRWWA_1

hyb_protocol: GRWWA_1 Cy5 / GRWWB_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: healthy people, biological replicate3

status: Public on Apr 04 2017

city: Changchun

first: Bo

middle: Fan

last: Meng

address: Xiantai Street 126 of Changchun of Jilin Province

country: China

institute: the Department of Cardiology, China–Japan Union Hospital, Jilin University,

description:
the total RNA was extracted from the leucocyte of peripheral blood
healthy people 3_3
Identical RMA signals in GSM2561554 and GSM1830992.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on HG-U133_Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Genechip Scanner 3000

data_processing:
The data were analyzed with robust multichip average method and present or absent calls of each probe set were determined by MAS5 method with affy package in R. The differentially genes between coronary heart disease and healthy groups were identified by performing moderated t-statistic in limma package, and the raw p values were adjusted by the FDR method.
P.Value≤0.05 and |logFC|>1

label: biotin

source_name: peripheral blood of healthy people

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA

growth_protocol: the peripheral blood were stored in 4℃ before extracting the total RNA

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

treatment_protocol: Two milliliter peripheral blood from each subject was collected into BD Vacutainer Single-use Containers for human venous blood specimen collection

tag: disease state

value: control

tag: tissue

value: peripheral blood

tag: genotype

value: Chinese

tag: age

value: 52 years


title: patients with acute myocardial infarction, biological replicate1

description:
the total RNA was extracted from the leucocyte of peripheral blood
patients 1_1

source_name: peripheral blood of patients with acute myocardial infarction

value: acute myocardial infarction

value: 39 years


title: 559665A02 - GRWSB_3 vs GRWWA_3

hyb_protocol: GRWWA_3 Cy5 / GRWSB_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 559665A07 - GRWSB_2 vs GRWWB_2

hyb_protocol: GRWWB_2 Cy5 / GRWSB_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 559665A04 - GRWSB_4 vs GRWWA_4

hyb_protocol: GRWWA_4 Cy5 / GRWSB_4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 549559A11 - GRWSB_2 vs GRWWA_2

hyb_protocol: GRWWA_2 Cy5 / GRWSB_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 559665A01 - GRWWA_3 vs GRWSB_3

hyb_protocol: GRWSB_3 Cy5 / GRWWA_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 559665A06 - GRWWB_1 vs GRWSB_1

hyb_protocol: GRWSB_1 Cy5 / GRWWB_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 549559A08 - GRWWA_4 vs GRWWB_4

hyb_protocol: GRWWB_4 Cy5 / GRWWA_4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: C17.2_10daysDifferentiation_E11

city: Stockholm

first: Kristina

last: Attoff

address: Svante Arrhenius väg 16C

country: Sweden

institute: Department of neurochemistry, Stockholm University

hyb_protocol: GeneChip® ST Arrays (GeneChip® Mouse Gene 2.1 ST 16-Array Plate) were hybridized for 16 hours in a 45°C incubator, washed and stained with the GeneTitan® Multi-Channel (MC) Instrument, according to the GeneTitan Instrument User Guide for Expression Arrays Plates (P/N 702933 Rev. 2, Affymetrix Inc., Santa Clara, CA).

scan_protocol: All samples were scanned with the GeneTitan® Multi-Channel (MC) Instrument, according to the GeneTitan Instrument User Guide for Expression Arrays Plates (P/N 702933 Rev. 2, Affymetrix Inc., Santa Clara, CA).

data_processing: The raw data was normalized in the free software Expression Console provided by Affymetrix (http://www.affymetrix.com) using the robust multi-array average (RMA) method first suggested by Li and Wong in 2001 (1,2)

organism: Mus musculus

source_name: C17.2 cells_differentiated for 10 days with NGF and BDNF

label_protocol: 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT PLUS Reagent Kit User Manual (P/N 703174 Rev. 1, Affymetrix Inc., Santa Clara, CA)

growth_protocol: The cells were cultured in DMEM supplemented with 5% horse serum, 10% fetal calf serum, 2 mM L-glutamine, 100 U penicillin/mL and 100 μg streptomycin/mL. The confluent cells were detached every 3rd and a half day using 0.05/0.02% trypsin/EDTA and seeded in a new cell culture Petri dish at the original density. For differentiation studies, the C17.2 cells were seeded in routine culture medium

extract_protocol: RNA extraction with the Qiagen Rneasy Plus Mini Kit according to manufacturer´s instructions

treatment_protocol: Twenty-four hours after seeding the medium was changed to DMEM/F-12 medium supplemented with 1 mM L-glutamine, 100 U penicillin/mL, 100 μg streptomycin/mL, modified N2 supplements (to a final concentration of 5 μg/mL bovine insulin, 20 nM progesterone, 30 nM sodium selenite, 100 μg/mL bovine apo-transferrin, and 100 μM putrescine dihydrochloride), 10 ng/mL NGF and 10 ng/mL BDNF. The differentiation medium was changed every 3rd day for the duration of the differentiation. The cells were kept in a humidified atmosphere of 5% CO2 in air at 37oC

tag: cell line

value: progenitor cell line

tag: cell status


title: 549559A05 - GRWWB_3 vs GRWWA_3

hyb_protocol: GRWWA_3 Cy5 / GRWWB_3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: healthy people, biological replicate2

description:
the total RNA was extracted from the leucocyte of peripheral blood
healthy people 3_2
Identical RMA signals in GSM2561553 and GSM1830991.

value: 50 years


title: C17.2_undifferentiated_B1

source_name: C17.2 cells_undifferentiated

value: undifferentiated


title: C17.2_5daysDifferentiation_B3

source_name: C17.2 cells_differentiated for 5 days with NGF and BDNF


title: C17.2_undifferentiated_E1


title: healthy people, biological replicate1

description:
the total RNA was extracted from the leucocyte of peripheral blood
healthy people 3_1
Identical RMA signals in GSM2561552 and GSM1830990.

value: 59 years


title: C17.2_5daysDifferentiation_C2

value: differentiated for 5 days with NGF and BDNF


title: 549559A07 - GRWWB_4 vs GRWWA_4

hyb_protocol: GRWWA_4 Cy5 / GRWWB_4 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: C17.2_5daysDifferentiation_E3


title: CD43neg A3.P0

city: Lund

first: Carolina

last: Guibentif

institute: Lund University

description: 1 cell

data_processing: Following the Biomark run, data was first analysed with Fluidigm Real-Time PCR Analysis Software, for evaluation of the amplification curves, and Ct thresholds were set automatically using the auto detector function.  Reactions with Ct>30 were considered negative. In assays where amplification was detected in no-RT controls, all reactions displaying Ct > [min(CtnoRTcontrols) – 2] were considered negative. The data was then analysed using the SCexV online tool http://stemsysbio.bmc.lu.se/SCexV/  (Lang et al., 2015) together with the Index-sort data, for performing principal component analysis (PCA) and hierarchical clustering based on the gene expression data. Cells displaying a Ct value >25 in the housekeeping gene GAPDH were excluded from the analysis, as well as the positive control samples. Subsequent analysis was then performed for the remaining cells (representing over 90% of the total sorted cells), using all assays and surface phenotype data excluding the housekeeping gene GAPDH.

label: FAM-MGB

source_name: plate 1

label_protocol: Pre-amplification mastermix (6.25 µl of 2X Reaction Buffer, 1 µl of SuperScript III RT/ Platinum Taq mix, and 1.5 µl of Taqman assays equal volume pool) was then added to each sample and reverse transcription was performed followed by pre-amplification in a Biorad T100 thermal cycler using the following program: 1h at 50ºC, 2 min at 95ºC and 25 cycles of 15 sec at 95ºC and 4 min at 60ºC. Pre-amplified samples were diluted 1:5 and run in Fluidigm 96.96 arrays on a Biomark device (Fluidigm), with Taqman universal MasterMix (Life Technologies) and the Taqman assays using the appropriate loading reagents according to manufacturer’s instructions.

growth_protocol: The iPS line was maintained in co-culture with irradiated murine embryonic fibroblasts in Dulbecco’s Modified Eagle Medium Nutrient Mixture F-12 supplemented with 20% KnockOut-serum replacement, Glutamax, Non-Essential Amino Acids, 50 µM beta-mercaptoethanol and 10 ng/mL Fgf2 (all from Life Technologies) in a humidified incubator at 37ºC, 5% CO2. Cells were passaged every six days using 1mg/ml Collagenase IV (Life Technologies). During two days preceding initiation of the blood differentiation protocol, the cultures were treated with 3 µM CHIR99021 (R&D Systems Europe).

extract_protocol: Single CD34+ cells were sorted directly into 96-well PCR plates (Sarstedt), using the Index-Sorting function of the Diva Software, into 4 µl of lysis buffer [65 µM of dNTP mix (Takara), 0.4% of NP40 Cell Lysis Buffer, 2.4 mM dithiothreitol, 0.5 U/µl RNAseOUT (Life Technologies) in nuclease-free water]. Target-specific pre-amplification was then performed using CellsDirect One-Step qRT-PCR Kit (Life Technologies).

treatment_protocol: Differentiation towards the blood lineage was performed as follows: the iPS colonies were incubated in 500 µg/ml Dispase (Life Technologies) for 40 minutes at 37ºC and resulting embryoid bodies (EBs) were transferred into ultra-low attachment culture dishes (Corning) in Mesototal medium (Primorigen Biosciences, Wisconsin). At day eight the EBs were plated on Matrigel-coated dishes (8 µg/cm2, Corning) in order to attach and spread a monolayer. Fresh Mesototal medium was added every second day throughout the protocol.

value: human iPS-derived CD34+

tag: cd43 phenotype

value: negative


title: CD43neg A2.P4

description: 1 cell

source_name: plate 5


title: CD43neg A2.P2

description: 1 cell

source_name: plate 3


title: 549559A03 - GRWWB_2 vs GRWWA_2

hyb_protocol: GRWWA_2 Cy5 / GRWWB_2 Cy3 : 30pmol. (Hybridation_affy.doc)


title: CD43neg A2.P3

description: 1 cell

source_name: plate 4


title: C17.2_10daysDifferentiation_B11

value: differentiated for 10 days with NGF and BDNF


title: C17.2_10daysDifferentiation_C6


title: 549559A04 - GRWWA_2 vs GRWWB_2

hyb_protocol: GRWWB_2 Cy5 / GRWWA_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: CD43neg A3.P2

description: 1 cell


title: CD43neg A12.P1

description: 1 cell

source_name: plate 2


title: CD43neg A12.P4

description: 1 cell


title: CD43neg A12.P0

description: 1 cell


title: 549559A02 - GRWWA_1 vs GRWWB_1

hyb_protocol: GRWWB_1 Cy5 / GRWWA_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: patients with acute myocardial infarction, biological replicate2

description:
the total RNA was extracted from the leucocyte of peripheral blood
patients 1_2

value: 55 years


title: C17.2_undifferentiated_C1


title: CD43neg A11.P1

description: 1 cell


title: CD43neg A11.P2

description: 1 cell


title: CD43neg A11.P3

description: 1 cell


title: CD43neg A2.P1

description: 1 cell


title: CD43neg A12.P2

description: 1 cell


title: CD43neg A10.P2

description: 1 cell


title: CD43neg A10.P0

description: 1 cell


title: CD43neg 10 cell linearity control.P0

description: 10 cells


title: CD43neg 10 cell linearity control.P2

description: 10 cells


title: patients with acute myocardial infarction, biological replicate3

description:
the total RNA was extracted from the leucocyte of peripheral blood
patients 1_3

value: 65 years


title: CD43neg A2.P0

description: 1 cell


title: CD43pos H9.P3

description: 1 cell

value: positive


title: CD43pos H8.P2

description: 1 cell


title: CD43neg A3.P1

description: 1 cell


title: CD43pos H8.P1

description: 1 cell


title: CD43pos H9.P2

description: 1 cell


title: CD43pos H8.P3

description: 1 cell


title: CD43pos H8.P0

description: 1 cell


title: CD43neg 10 cell linearity control.P4

description: 10 cells


title: CD43neg A12.P3

description: 1 cell


title: CD43neg A11.P0

description: 1 cell


title: CD43neg A10.P3

description: 1 cell


title: CD43neg A10.P4

description: 1 cell


title: CD43neg A10.P1

description: 1 cell


title: CD43pos H7.P0

description: 1 cell


title: CD43neg 10 cell linearity control.P1

description: 10 cells


title: CD43pos H6.P3

description: 1 cell


title: CD43pos H9.P0

description: 1 cell


title: CD43pos H8.P4

description: 1 cell


title: CD43neg A11.P4

description: 1 cell


title: CD43pos H6.P2

description: 1 cell


title: CD43neg 10 cell linearity control.P3

description: 10 cells


title: CD43pos H9.P4

description: 1 cell


title: CD43pos H9.P1

description: 1 cell


title: CD43pos H5.P0

description: 1 cell


title: CD43pos H3.P2

description: 1 cell


title: CD43pos H7.P4

description: 1 cell


title: CD43pos H3.P1

description: 1 cell


title: CD43pos H4.P1

description: 1 cell


title: CD43pos H3.P4

description: 1 cell


title: CD43pos H3.P0

description: 1 cell


title: CD43pos H2.P3

description: 1 cell


title: CD43pos H2.P2

description: 1 cell


title: CD43pos H5.P2

description: 1 cell


title: 559665A05 - GRWSB_1 vs GRWWB_1

hyb_protocol: GRWWB_1 Cy5 / GRWSB_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: Pisum sativum L  - harvest date:03-02-14


title: CD43pos H12.P1

description: 1 cell


title: CD43pos H7.P1

description: 1 cell


title: CD43pos H6.P1

description: 1 cell


title: CD43pos H2.P0

description: 1 cell


title: CD43pos H7.P2

description: 1 cell


title: CD43pos H2.P1

description: 1 cell


title: CD43pos H7.P3

description: 1 cell


title: CD43pos H6.P4

description: 1 cell


title: CD43pos H6.P0

description: 1 cell


title: CD43pos H12.P4

description: 1 cell


title: CD43pos H5.P4

description: 1 cell


title: CD43pos H11.P1

description: 1 cell


title: CD43pos H4.P4

description: 1 cell


title: CD43pos H11.P4

description: 1 cell


title: CD43pos H10.P2

description: 1 cell


title: CD43pos H5.P3

description: 1 cell


title: CD43pos H5.P1

description: 1 cell


title: CD43pos G8.P4

description: 1 cell


title: CD43pos G9.P3

description: 1 cell


title: CD43pos H4.P0

description: 1 cell


title: CD43pos H4.P3

description: 1 cell


title: CD43pos G8.P3

description: 1 cell


title: CD43pos G8.P1

description: 1 cell


title: CD43pos G8.P2

description: 1 cell


title: CD43pos H4.P2

description: 1 cell


title: CD43pos G9.P4

description: 1 cell


title: CD43pos H2.P4

description: 1 cell


title: CD43pos H12.P3

description: 1 cell


title: CD43pos H11.P3

description: 1 cell


title: CD43pos G7.P2

description: 1 cell


title: CD43pos G7.P1

description: 1 cell


title: CD43pos H3.P3

description: 1 cell


title: CD43pos G8.P0

description: 1 cell


title: CD43pos H12.P0

description: 1 cell


title: CD43pos G9.P2

description: 1 cell


title: CD43pos G6.P3

description: 1 cell


title: CD43pos H11.P0

description: 1 cell


title: CD43pos H10.P1

description: 1 cell


title: CD43pos H10.P4

description: 1 cell


title: CD43pos H10.P3

description: 1 cell


title: CD43pos G9.P0

description: 1 cell


title: CD43pos G5.P1

description: 1 cell


title: CD43pos G6.P0

description: 1 cell


title: CD43pos G9.P1

description: 1 cell


title: CD43pos G4.P3

description: 1 cell


title: CD43pos G7.P4

description: 1 cell


title: CD43pos G5.P0

description: 1 cell


title: CD43pos H10.P0

description: 1 cell


title: CD43pos G7.P3

description: 1 cell


title: CD43pos G4.P0

description: 1 cell


title: CD43pos G7.P0

description: 1 cell


title: CD43pos G6.P2

description: 1 cell


title: CD43pos G3.P1

description: 1 cell


title: CD43pos G5.P2

description: 1 cell


title: CD43pos G5.P4

description: 1 cell


title: CD43pos H11.P2

description: 1 cell


title: CD43pos G2.P3

description: 1 cell


title: CD43pos G4.P2

description: 1 cell


title: CD43pos G6.P1

description: 1 cell


title: CD43pos G6.P4

description: 1 cell


title: CD43pos G12.P4

description: 1 cell


title: CD43pos G11.P2

description: 1 cell


title: CD43pos G3.P3

description: 1 cell


title: CD43pos G11.P4

description: 1 cell


title: CD43pos G11.P0

description: 1 cell


title: CD43pos G5.P3

description: 1 cell


title: CD43pos G10.P4

description: 1 cell


title: CD43pos G10.P0

description: 1 cell


title: CD43pos G10.P2

description: 1 cell


title: CD43pos F9.P4

description: 1 cell


title: CD43pos G2.P2

description: 1 cell


title: CD43pos G4.P1

description: 1 cell


title: CD43pos G12.P0

description: 1 cell


title: CD43pos G3.P0

description: 1 cell


title: CD43pos G2.P4

description: 1 cell


title: CD43pos F9.P0

description: 1 cell


title: CD43pos G2.P1

description: 1 cell


title: CD43pos G4.P4

description: 1 cell


title: CD43pos F8.P2

description: 1 cell


title: CD43pos F9.P1

description: 1 cell


title: CD43pos G3.P4

description: 1 cell


title: CD43pos G2.P0

description: 1 cell


title: CD43pos G3.P2

description: 1 cell


title: CD43pos G12.P3

description: 1 cell


title: CD43pos F9.P2

description: 1 cell


title: CD43pos G10.P3

description: 1 cell


title: CD43pos G11.P1

description: 1 cell


title: CD43pos F7.P4

description: 1 cell


title: CD43pos F7.P0

description: 1 cell


title: CD43pos G12.P2

description: 1 cell


title: CD43pos G11.P3

description: 1 cell


title: CD43pos G10.P1

description: 1 cell


title: CD43pos F9.P3

description: 1 cell


title: CD43pos F7.P2

description: 1 cell


title: CD43pos F6.P3

description: 1 cell


title: CD43pos F6.P4

description: 1 cell


title: CD43pos F5.P2

description: 1 cell


title: CD43pos F8.P3

description: 1 cell


title: CD43pos F8.P4

description: 1 cell


title: CD43pos F8.P1

description: 1 cell


title: CD43pos F5.P3

description: 1 cell


title: CD43pos F5.P4

description: 1 cell


title: CD43pos F5.P1

description: 1 cell


title: CD43pos F6.P2

description: 1 cell


title: CD43pos F5.P0

description: 1 cell


title: CD43pos G12.P1

description: 1 cell


title: CD43pos F6.P0

description: 1 cell


title: CD43pos F8.P0

description: 1 cell


title: CD43pos F4.P2

description: 1 cell


title: CD43pos F4.P3

description: 1 cell


title: CD43pos F4.P4

description: 1 cell


title: CD43pos F7.P1

description: 1 cell


title: CD43pos F4.P0

description: 1 cell


title: CD43pos F6.P1

description: 1 cell


title: CD43pos F7.P3

description: 1 cell


title: CD43pos F12.P3

description: 1 cell


title: CD43pos F3.P4

description: 1 cell


title: CD43pos F3.P3

description: 1 cell


title: CD43pos F2.P1

description: 1 cell


title: CD43pos F4.P1

description: 1 cell


title: CD43pos F12.P2

description: 1 cell


title: CD43pos F3.P1

description: 1 cell


title: CD43pos F2.P4

description: 1 cell


title: CD43pos F2.P2

description: 1 cell


title: CD43pos F3.P2

description: 1 cell


title: CD43pos F12.P4

description: 1 cell


title: CD43pos F11.P4

description: 1 cell


title: CD43pos F10.P2

description: 1 cell


title: CD43pos F11.P1

description: 1 cell


title: CD43pos F11.P0

description: 1 cell


title: CD43pos F3.P0

description: 1 cell


title: CD43pos F12.P0

description: 1 cell


title: CD43pos F10.P0

description: 1 cell


title: CD43pos F2.P0

description: 1 cell


title: CD43pos F10.P1

description: 1 cell


title: CD43pos F10.P3

description: 1 cell


title: CD43pos F10.P4

description: 1 cell


title: CD43pos E9.P4

description: 1 cell


title: CD43pos F2.P3

description: 1 cell


title: CD43pos F12.P1

description: 1 cell


title: CD43pos E9.P3

description: 1 cell


title: CD43pos F11.P3

description: 1 cell


title: CD43pos F11.P2

description: 1 cell


title: CD43pos E9.P2

description: 1 cell


title: CD43pos E9.P0

description: 1 cell


title: hepatocellular carcinoma(HCC) tumor tissue circRNA 7

city: HANGZHOU

first: DAN

last: HAN

state: ZHEJIANG

address: 866 YUHANGTANG ROAD

department: MEDICAL COLLEGE

institute: ZHEJIANG UNIVERSITY

description:
T74013
circRNA expression hepatocellular carcinoma(HCC) tumor tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: HCC and matched non-tumor hepar tissues

treatment_protocol: Tissues from HCC surgury and promptly frozen in liquid nitrogen.

value: HCC tumor tissue

tag: gender

value: male


title: hepatocellular carcinoma(HCC) tumor tissue circRNA 5

description:
T74000
circRNA expression hepatocellular carcinoma(HCC) tumor tissue


title: CD43pos E9.P1

description: 1 cell


title: CD43pos E8.P1

description: 1 cell


title: CD43pos E8.P4

description: 1 cell


title: hepatocellular carcinoma(HCC) tumor tissue circRNA 4

description:
T73970
circRNA expression hepatocellular carcinoma(HCC) tumor tissue


title: CD43pos E8.P0

description: 1 cell


title: CD43pos E8.P3

description: 1 cell


title: CD43pos E8.P2

description: 1 cell


title: CD43pos E7.P2

description: 1 cell


title: hepar normal tissue circRNA 5

description:
N74000
circRNA expression data from Homo sapiens hepar

source_name: hepar normal tissue

value: normal hepar tissue from HCC


title: hepatocellular carcinoma(HCC) tumor tissue circRNA 3

description:
T73936
circRNA expression hepatocellular carcinoma(HCC) tumor tissue


title: CD43pos E7.P1

description: 1 cell


title: hepatocellular carcinoma(HCC) tumor tissue circRNA 2

description:
T69749
circRNA expression hepatocellular carcinoma(HCC) tumor tissue


title: hepar normal tissue circRNA 6

description:
N74009
circRNA expression data from Homo sapiens hepar


title: hepar normal tissue circRNA 7

description:
N74013
circRNA expression data from Homo sapiens hepar


title: hepatocellular carcinoma(HCC) tumor tissue circRNA 6

description:
T74009
circRNA expression hepatocellular carcinoma(HCC) tumor tissue


title: CD43pos E7.P4

description: 1 cell


title: CD43pos E6.P4

description: 1 cell


title: hepar normal tissue circRNA 3

description:
N73936
circRNA expression data from Homo sapiens hepar


title: hepar normal tissue circRNA 2

description:
N69749
circRNA expression data from Homo sapiens hepar


title: CD43pos E7.P0

description: 1 cell


title: CD43pos E6.P3

description: 1 cell


title: CD43pos E7.P3

description: 1 cell


title: hepar normal tissue circRNA 1

description:
L72763
circRNA expression data from Homo sapiens hepar


title: CD43pos E6.P2

description: 1 cell


title: hepatocellular carcinoma(HCC) tumor tissue circRNA 1

description:
T72763
circRNA expression hepatocellular carcinoma(HCC) tumor tissue


title: CD43pos E6.P1

description: 1 cell


title: hepar normal tissue circRNA 4

description:
N73970
circRNA expression data from Homo sapiens hepar


title: CD43pos E6.P0

description: 1 cell


title: CD43pos E5.P4

description: 1 cell


title: CD43pos E5.P3

description: 1 cell


title: CD43pos E5.P2

description: 1 cell


title: Lame83 Area3 Data

city: Québec

first: Anne-Laure

last: Nivet

state: Québec

address: 2440 Hochelaga Blvd

country: Canada

institute: Laval University

description: Array 6

hyb_protocol: hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Embryogene ELMA application was used.

organism: Bos taurus

source_name: ctrl

label_protocol:
amplification protocol: amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
Tlabelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: conditions RNAse free; 3 rincages PBS  sterile; centrifugation 3000 rpm 4-5 mintes; snap freezeat -80

extract_protocol: total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.

tag: breed (cattle)

value: holstein

tag: follicular size

value: Pre-ovulatory

tag: cell collection method

value: aspiration

tag: follicular status

value: coasted

tag: in vitro production

value: Yes

tag: time

value: 68 hours

tag: exogenous hormone ovarian stimulation

value: Gonadotropins

tag: reproductive status (cattle)

value: Multiparity

tag: tissue or cell type

value: granulosa

source_name: cetrotide


title: CD43pos E5.P0

description: 1 cell

tag: cell type

value: human iPS-derived CD34+


title: Lama84 Area2 Data

description: Array 2

tag: sample type


title: CD43pos E4.P4

description: 1 cell


title: Lame83 Area2 Data

description: Array 5


title: CD43pos E4.P3

description: 1 cell


title: CD43pos E4.P1

description: 1 cell


title: CD43pos E4.P0

description: 1 cell


title: CD43pos E3.P4

description: 1 cell


title: Lama84 Area1 Data

description: Array 1


title: Lame83 Area1 Data

description: Array 4


title: CD43pos E3.P3

description: 1 cell


title: CD43pos E5.P1

description: 1 cell


title: DBA_Rpl35A_R3_mut_44_2

city: Little Rock

first: Jason

middle: Eli

last: Farrar

state: AR

address: 1 Children's Way, #512-10

department: Pediatrics/Hematology-Oncology

country: USA

institute: University of Arkansas for Medical Sciences

description: subject R3

hyb_protocol: Labeled cDNA was hybridized to Human Gene 2.0 ST arrays according to the manufacturer’s instructions.

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing: Gene-level expression data were summarized after background correction and RMA normalization using the 'Oligo'  Bioconductor package

source_name: Cultured erythroid progenitor

label_protocol: cDNA prepared by WT Plus Expression Kit (Affymetrix) from 200 ng of RNA.

growth_protocol: CD34+ cells were collected in ACD from peripheral blood. Mononuclear cells were separated by centrifugation on lymphocyte separation media (MP Biomedicals), and CD34+ cells were isolated by using a CD34 microbead kit (Miltenyi Biotec) and an autoMACS Separator (Miltenyi Biotec). CD34+ cells were cultured in a 2-step erythroid culture over  2 weeks. Briefly, cells were cultured for 7 days in proliferation media consisting of StemSpan Serum-Free Expansion Medium (Stemcell Technologies) supplemented with penicillin/streptomycin 100U/mL, Glutamine 2mM, human LDL  40ug/mL, and the following cytokines: stem cell factor 100 ng/mL, thrombopoietin 50 ng/mL, IL-3 10 ng/mL, IL-6 10 ng/mL, Erythropoietin  0.5 U/mL. After 7 days, cells were cultured in expansion media consisting of proliferation media with 3 U/mL Erythropoietin for an additional 7 days.

extract_protocol: RNA was extracted using the Purelink RNA kit (Life Technologies).

value: Cultured erythroid progenitor

tag: patient phenotype

value: Diamond Blackfan anemia

tag: genotype

tag: cell population


title: DBA_Rps24_R4_mut_44

description: subject R4


title: DBA_Rpl35A_R3_mut_235_2

description: subject R3


title: DBA_Rpl35A_R3_mut_235

description: subject R3


title: Lama84 Area3 Data

description: Array 3


title: CD43pos E3.P2

description: 1 cell

value: positive


title: CD43pos E3.P1

description: 1 cell


title: DBA_Rps17_R5_mut_44

description: subject R5


title: DBA_Rpl35A_R3_mut_44

description: subject R3


title: Normal_N/A_N8_mut_44

description: subject N8

value: Normal


title: DBA_Rpl5_R2_mut_44

description: subject R2


title: CD43pos E4.P2

description: 1 cell


title: DBA_Rps17_R1_mut_44

description: subject R1


title: Normal_N/A_N7_mut_44

description: subject N7


title: CD43pos E2.P4

description: 1 cell


title: CD43pos E2.P3

description: 1 cell


title: CD43pos E2.P2

description: 1 cell


title: Normal_N/A_N5_mut_235

description: subject N5


title: Normal_N/A_N7_mut_235

description: subject N7


title: Normal_N/A_N9_mut_235

description: subject N9


title: Normal_N/A_N6_mut_44

description: subject N6


title: CD43pos E3.P0

description: 1 cell


title: Normal_N/A_N5_mut_44

description: subject N5


title: Normal_N/A_N4_mut_44

description: subject N4


title: Normal_N/A_N6_mut_235

description: subject N6


title: CD43pos E12.P3

description: 1 cell


title: CD43pos E2.P0

description: 1 cell


title: Normal_N/A_N3_mut_235

description: subject N3


title: Normal_N/A_N2_mut_44

description: subject N2


title: Normal_N/A_N3_mut_44

description: subject N3


title: CD43pos E12.P4

description: 1 cell


title: CD43pos E11.P4

description: 1 cell


title: CD43pos E12.P1

description: 1 cell


title: CD43pos E12.P2

description: 1 cell


title: CD43pos E12.P0

description: 1 cell


title: Normal_N/A_N1_mut_44

description: subject N1


title: Normal_N/A_N2_mut_235_2

description: subject N2


title: Normal_N/A_N10_mut_235

description: subject N10


title: CD43pos E11.P2

description: 1 cell


title: Normal_N/A_N2_mut_235

description: subject N2


title: Normal_N/A_N1_mut_235

description: subject N1


title: CD43pos E11.P3

description: 1 cell


title: DBA_Indeterminate_I4_mut_44

description: subject I4

value: Indeterminate


title: DBA_Indeterminate_I4_mut_235

description: subject I4


title: CD43pos E10.P3

description: 1 cell


title: CD43pos E11.P0

description: 1 cell


title: DBA_Indeterminate_I3_mut_44_2

description: subject I3


title: DBA_Indeterminate_I2_mut_44

description: subject I2


title: DBA_Indeterminate_I3_mut_44

description: subject I3


title: CD43pos E10.P4

description: 1 cell


title: CD43pos E11.P1

description: 1 cell


title: CD43pos E10.P0

description: 1 cell


title: CD43pos 10cell linearity control.P3

description: 10 cells


title: CD43pos 10cell linearity control.P1

description: 10 cells


title: DBA_Gata1_G2_mut_44

description: subject G2


title: CD43pos 10cell linearity control.P2

description: 10 cells


title: DBA_Indeterminate_I1_mut_44

description: subject I1


title: DBA_Gata1_G1_mut_235

description: subject G1


title: DBA_Indeterminate_I1_mut_235

description: subject I1


title: CD43pos 10cell linearity control.P4

description: 10 cells


title: DBA_Gata1_G1_mut_44_2

description: subject G1


title: CD43pos E10.P2

description: 1 cell


title: CD43pos E10.P1

description: 1 cell


title: DBA_Gata1_G1_mut_44

description: subject G1


title: CD43pos 10cell linearity control.P0

description: 10 cells


title: CD43neg D9.P4

description: 1 cell

value: negative


title: Solvent control to Bovine macrophages at 24h_trial#3

city: Guelph

first: Se-Young

last: Oh

state: Ontario

address: 50 Stone Rd East

department: Animal Bioscience

institute: University of Guelph

description: Gene expression data from bovine macrophage cell line exposed to ethanol only for 24 hours from trial#3

hyb_protocol: Labeled cRNA was hybridized to Affymetrix Bovine Gene 1.0 ST Array for 16 h at 45°C, followed by washing and staining.

scan_protocol: Affymetrix GeneChips were scanned using an Affymetrix GeneChip® Scanner 3000 7G

data_processing: Affymetrix Expression Console software was used to normalize the data. Subsequently, the dataset was analyzed using the Affymetrix Transcriptome Analysis Console software (cluster analysis and relative expression was performed)

label: Biotin

source_name: BoMac after 24 hours of EC (solvent control) exposure

label_protocol: Biotin-Labeled cRNA for all samples was made according to package directions (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Bovine macrophage cell line (1.0 x 106) were seeded into six-well flat-bottom plates (Corning Inc., U.S.A), centrifuged for 2 min at 100 g, and incubated at 37ºC with 5% CO2.

extract_protocol: total RNA was extracted using the RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen, Toronto, Ontario)

treatment_protocol: After 1 h of incubation, the cells were exposed to ochratoxin A (OTA) and citrinin (CIT) at their respective IC25 (the concentration that inhibit 25% of cell proliferation), which was determined from a previous study with BoMac (Oh et al. 2012; Open Mycol. J. 6, 11–16). Three PM treatments (OTA, CIT, and co-exposure of OTA+ CIT) were used, as well as a solvent control (ethanol equivalent to the highest treatment concentration) for each time point.

value: macrophage

tag: treatment

value: exposed to ethanol only for 24 hours


title: 57-MDD-L5-4

city: Pittsburgh

first: David

last: Lewis

state: PA

address: 3811 O'Hara St

department: Psychiatry and Neuroscience

institute: University of Pittsburgh

description: Gene expression data for subject 57, diagnosis MDD, layer 5, replicate 2

hyb_protocol: CDNA was synthesized and amplified using the Ovation Pico WTA System.

scan_protocol: Loaded on an Affymetrix GeneChip® U219.

data_processing: Expression intensities were extracted from Affymetrix Expression Console and normalized using Robust Multi-array Average Express.

label: Encore Biotin module (Nugen)

source_name: dorsolateral prefrontal cortex

label_protocol: Labeled using the Encore Biotin module (Nugen).

growth_protocol: Brain specimens were obtained during autopsies conducted at the Allegheny County Office of the Medical Examiner (Pittsburgh, PA) after consent was obtained from the next-of-kin.

extract_protocol: For each sample, RNA was extracted using the QIAGEN® RNeasy Plus Micro kit (QIAGEN, Valencia).

treatment_protocol: An independent committee of experienced research clinicians made consensus DSM-IV diagnoses for each subject using information obtained from medical records and structured diagnostic interviews conducted with the decedent’s family members.

tag: tissue

value: dorsolateral prefrontal cortex

value: pyramidal neuron cell

tag: shape

value: characteristic triangular shape and prominent apical dendrite

value: Major Depressive Disorder

tag: dsm-iv diagnoses

value: MDD, recurrent


title: 74-SZ-L3-1

description: Gene expression data for subject 74, diagnosis SZ, layer 3, replicate 1

value: Schizophrenia

value: US


title: CD43neg D9.P2

description: 1 cell

tag: cd43 phenotype


title: 74-SZ-L5-3

description: Gene expression data for subject 74, diagnosis SZ, layer 5, replicate 1


title: 74-SZ-L5-4

description: Gene expression data for subject 74, diagnosis SZ, layer 5, replicate 2


title: 57-MDD-L5-3

description: Gene expression data for subject 57, diagnosis MDD, layer 5, replicate 1


title: CD43neg D9.P3

description: 1 cell


title: 74-SZ-L3-2

description: Gene expression data for subject 74, diagnosis SZ, layer 3, replicate 2


title: 57-MDD-L3-2

description: Gene expression data for subject 57, diagnosis MDD, layer 3, replicate 2


title: OTA exposure to Bovine macrophages at 24h_trial#3

description: Gene expression data from bovine macrophage cell line exposed to OTA for 24 hours from trial#3

source_name: BoMac after 24 hours of OTA exposure

value: exposed to OTA for 24 hours


title: CIT exposure to Bovine macrophages at 24h_trial#3

description: Gene expression data from bovine macrophage cell line exposed to CIT for 24 hours from trial#3.

source_name: BoMac after 24 hours of CIT exposure

value: exposed to CIT for 24 hours


title: 38-BP-L5-4

description: Gene expression data for subject 38, diagnosis BP, layer 5, replicate 2

value: Bipolar

value: Bipolar I; AAC


title: 19-UC-L5-3

description: Gene expression data for subject 19, diagnosis UC, layer 5, replicate 1

value: Unaffected Comparison subject

value: Unaffected Comparison


title: 57-MDD-L3-1

description: Gene expression data for subject 57, diagnosis MDD, layer 3, replicate 1


title: 19-UC-L3-2

description: Gene expression data for subject 19, diagnosis UC, layer 3, replicate 2


title: Solvent control to Bovine macrophages at 6h_trial#3

description: Gene expression data from bovine macrophage cell line exposed to ethanol only for 6 hours from trial#3

source_name: BoMac after 6 hours of EC (solvent control) exposure

value: exposed to ethanol only for 6 hours


title: CIT+OTA coexposure to Bovine macrophages at 24h_trial#3

description: Gene expression data from bovine macrophage cell line coexposed to CIT and OTA for 24 hours from trial#3

source_name: BoMac after 24 hours of CIT+OTA coexposure

value: coexposed to CIT and OTA for 24 hours


title: CIT+OTA coexposure to Bovine macrophages at 6h_trial#3

description: Gene expression data from bovine macrophage cell line coexposed to CIT and OTA for 6 hours from trial#3

source_name: BoMac after 6 hours of CIT+OTA coexposure

value: macrophage

value: coexposed to CIT and OTA for 6 hours


title: CD43neg D9.P1

description: 1 cell

value: human iPS-derived CD34+

value: negative


title: CD43neg D8.P4

description: 1 cell


title: CD43neg D9.P0

description: 1 cell


title: CD43pos E2.P1

description: 1 cell

value: positive


title: CD43neg D8.P3

description: 1 cell


title: Normal_N/A_N4_mut_235

description: subject N4

value: Cultured erythroid progenitor

value: Normal


title: OTA exposure to Bovine macrophages at 6h_trial#3

description: Gene expression data from bovine macrophage cell line exposed to OTA for 6 hours from trial#3

source_name: BoMac after 6 hours of OTA exposure

value: exposed to OTA for 6 hours


title: 38-BP-L3-1

description: Gene expression data for subject 38, diagnosis BP, layer 3, replicate 1

value: dorsolateral prefrontal cortex

value: pyramidal neuron cell

value: characteristic triangular shape and prominent apical dendrite


title: 56-MDD-L5-3

description: Gene expression data for subject 56, diagnosis MDD, layer 5, replicate 1

value: Major Depressive Disorder

value: MDD


title: CD43neg D8.P1

description: 1 cell


title: CD43neg D8.P2

description: 1 cell


title: 38-BP-L5-3

description: Gene expression data for subject 38, diagnosis BP, layer 5, replicate 1

value: Bipolar

value: Bipolar I; AAC


title: 38-BP-L3-2

description: Gene expression data for subject 38, diagnosis BP, layer 3, replicate 2


title: 56-MDD-L5-4

description: Gene expression data for subject 56, diagnosis MDD, layer 5, replicate 2


title: 73-SZ-L5-3

description: Gene expression data for subject 73, diagnosis SZ, layer 5, replicate 1

value: Schizophrenia

value: SA; ODC


title: 73-SZ-L5-4

description: Gene expression data for subject 73, diagnosis SZ, layer 5, replicate 2


title: CIT+OTA coexposure to Bovine macrophages at 24h_trial#2

description: Gene expression data from bovine macrophage cell line coexposed to CIT and OTA for 24 hours from trial#2

value: macrophage

value: coexposed to CIT and OTA for 24 hours


title: 73-SZ-L3-2

description: Gene expression data for subject 73, diagnosis SZ, layer 3, replicate 2


title: Solvent control to Bovine macrophages at 24h_trial#2

description: Gene expression data from bovine macrophage cell line exposed to ethanol only for 24 hours from trial#2

value: exposed to ethanol only for 24 hours


title: CIT exposure to Bovine macrophages at 24h_trial#2

description: Gene expression data from bovine macrophage cell line exposed to CIT for 24 hours from trial#2.

value: exposed to CIT for 24 hours


title: 18-UC-L3-2

description: Gene expression data for subject 18, diagnosis UC, layer 3, replicate 2

value: Unaffected Comparison subject

value: Unaffected Comparison


title: CIT exposure to Bovine macrophages at 6h_trial#3

description: Gene expression data from bovine macrophage cell line exposed to CIT for 6 hours from trial#3.

source_name: BoMac after 6 hours of CIT exposure

value: exposed to CIT for 6 hours


title: 73-SZ-L3-1

description: Gene expression data for subject 73, diagnosis SZ, layer 3, replicate 1


title: 56-MDD-L3-1

description: Gene expression data for subject 56, diagnosis MDD, layer 3, replicate 1


title: 18-UC-L5-4

description: Gene expression data for subject 18, diagnosis UC, layer 5, replicate 2


title: 56-MDD-L3-2

description: Gene expression data for subject 56, diagnosis MDD, layer 3, replicate 2


title: 18-UC-L5-3

description: Gene expression data for subject 18, diagnosis UC, layer 5, replicate 1


title: 19-UC-L3-1

description: Gene expression data for subject 19, diagnosis UC, layer 3, replicate 1


title: OTA exposure to Bovine macrophages at 24h_trial#2

description: Gene expression data from bovine macrophage cell line exposed to OTA for 24 hours from trial#2

value: exposed to OTA for 24 hours


title: 37-BP-L5-4

description: Gene expression data for subject 37, diagnosis BP, layer 5, replicate 2

value: dorsolateral prefrontal cortex

value: Bipolar I, PF


title: 18-UC-L3-1

description: Gene expression data for subject 18, diagnosis UC, layer 3, replicate 1

value: pyramidal neuron cell

value: characteristic triangular shape and prominent apical dendrite


title: CD43neg D8.P0

description: 1 cell

source_name: plate 1

value: human iPS-derived CD34+

value: negative


title: Solvent control to Bovine macrophages at 6h_trial#2

description: Gene expression data from bovine macrophage cell line exposed to ethanol only for 6 hours from trial#2

value: exposed to ethanol only for 6 hours


title: CD43neg D7.P4

description: 1 cell

source_name: plate 5


title: CD43neg D7.P2

description: 1 cell

source_name: plate 3


title: CD43neg D7.P3

description: 1 cell

source_name: plate 4


title: CIT+OTA coexposure to Bovine macrophages at 6h_trial#2

description: Gene expression data from bovine macrophage cell line coexposed to CIT and OTA for 6 hours from trial#2

value: coexposed to CIT and OTA for 6 hours


title: OTA exposure to Bovine macrophages at 6h_trial#2

description: Gene expression data from bovine macrophage cell line exposed to OTA for 6 hours from trial#2

value: exposed to OTA for 6 hours


title: 37-BP-L5-3

description: Gene expression data for subject 37, diagnosis BP, layer 5, replicate 1

value: Bipolar


title: 37-BP-L3-2

description: Gene expression data for subject 37, diagnosis BP, layer 3, replicate 2


title: 37-BP-L3-1

description: Gene expression data for subject 37, diagnosis BP, layer 3, replicate 1


title: 72-SZ-L3-1

description: Gene expression data for subject 72, diagnosis SZ, layer 3, replicate 1

value: Schizophrenia

value: US; ADR


title: CD43neg D7.P1

description: 1 cell

source_name: plate 2


title: CIT exposure to Bovine macrophages at 6h_trial#2

description: Gene expression data from bovine macrophage cell line exposed to CIT for 6 hours from trial#2.

value: macrophage


title: CD43neg D7.P0

description: 1 cell


title: 72-SZ-L3-2

description: Gene expression data for subject 72, diagnosis SZ, layer 3, replicate 2


title: 72-SZ-L5-3

description: Gene expression data for subject 72, diagnosis SZ, layer 5, replicate 1


title: Solvent control to Bovine macrophages at 24h_trial#1

description: Gene expression data from bovine macrophage cell line exposed to ethanol only for 24 hours from trial#1

value: exposed to ethanol only for 24 hours


title: 55-MDD-L5-4

description: Gene expression data for subject 55, diagnosis MDD, layer 5, replicate 2

value: Major Depressive Disorder

value: MDD, recurrent, PF


title: 17-UC-L3-2

description: Gene expression data for subject 17, diagnosis UC, layer 3, replicate 2

value: Unaffected Comparison subject

value: Unaffected Comparison


title: 17-UC-L5-4

description: Gene expression data for subject 17, diagnosis UC, layer 5, replicate 2

value: dorsolateral prefrontal cortex


title: 55-MDD-L3-1

description: Gene expression data for subject 55, diagnosis MDD, layer 3, replicate 1

value: pyramidal neuron cell


title: 17-UC-L3-1

description: Gene expression data for subject 17, diagnosis UC, layer 3, replicate 1

value: characteristic triangular shape and prominent apical dendrite


title: 55-MDD-L5-3

description: Gene expression data for subject 55, diagnosis MDD, layer 5, replicate 1


title: CD43neg D6.P4

description: 1 cell

value: human iPS-derived CD34+


title: CD43neg D6.P2

description: 1 cell

value: negative


title: OTA exposure to Bovine macrophages at 24h_trial#1

description: Gene expression data from bovine macrophage cell line exposed to OTA for 24 hours from trial#1

value: exposed to OTA for 24 hours


title: CIT exposure to Bovine macrophages at 24h_trial#1

description: Gene expression data from bovine macrophage cell line exposed to CIT for 24 hours from trial#1.

value: exposed to CIT for 24 hours


title: CD43neg D6.P3

description: 1 cell


title: 55-MDD-L3-2

description: Gene expression data for subject 55, diagnosis MDD, layer 3, replicate 2


title: CD43neg D6.P0

description: 1 cell


title: CIT+OTA coexposure to Bovine macrophages at 6h_trial#1

description: Gene expression data from bovine macrophage cell line coexposed to CIT and OTA for 6 hours from trial#1

value: coexposed to CIT and OTA for 6 hours


title: CD43neg D5.P4

description: 1 cell


title: CIT+OTA coexposure to Bovine macrophages at 24h_trial#1

description: Gene expression data from bovine macrophage cell line coexposed to CIT and OTA for 24 hours from trial#1

value: coexposed to CIT and OTA for 24 hours


title: 36-BP-L3-1

description: Gene expression data for subject 36, diagnosis BP, layer 3, replicate 1

value: Bipolar

value: Bipolar I, PF


title: 71-SZ-L3-1

description: Gene expression data for subject 71, diagnosis SZ, layer 3, replicate 1

value: Schizophrenia

value: SA; ADC


title: 54-MDD-L5-4

description: Gene expression data for subject 54, diagnosis MDD, layer 5, replicate 2

value: Major Depressive Disorder

value: MDD, recurrent; ADR; ODC


title: 71-SZ-L5-4

description: Gene expression data for subject 71, diagnosis SZ, layer 5, replicate 2


title: Solvent control to Bovine macrophages at 6h_trial#1

description: Gene expression data from bovine macrophage cell line exposed to ethanol only for 6 hours from trial#1

value: macrophage

value: exposed to ethanol only for 6 hours


title: 17-UC-L5-3

description: Gene expression data for subject 17, diagnosis UC, layer 5, replicate 1

value: dorsolateral prefrontal cortex

value: Unaffected Comparison subject

value: Unaffected Comparison


title: 36-BP-L3-2

description: Gene expression data for subject 36, diagnosis BP, layer 3, replicate 2

value: pyramidal neuron cell

value: characteristic triangular shape and prominent apical dendrite


title: CD43neg D5.P2

description: 1 cell

value: human iPS-derived CD34+

value: negative


title: 36-BP-L5-3

description: Gene expression data for subject 36, diagnosis BP, layer 5, replicate 1


title: 71-SZ-L3-2

description: Gene expression data for subject 71, diagnosis SZ, layer 3, replicate 2


title: 54-MDD-L3-2

description: Gene expression data for subject 54, diagnosis MDD, layer 3, replicate 2


title: 36-BP-L5-4

description: Gene expression data for subject 36, diagnosis BP, layer 5, replicate 2


title: 16-UC-L5-3

description: Gene expression data for subject 16, diagnosis UC, layer 5, replicate 1


title: 71-SZ-L5-3

description: Gene expression data for subject 71, diagnosis SZ, layer 5, replicate 1


title: CD43neg D6.P1

description: 1 cell


title: 16-UC-L3-2

description: Gene expression data for subject 16, diagnosis UC, layer 3, replicate 2


title: OTA exposure to Bovine macrophages at 6h_trial#1

description: Gene expression data from bovine macrophage cell line exposed to OTA for 6 hours from trial#1

value: exposed to OTA for 6 hours


title: CD43neg D4.P3

description: 1 cell


title: 16-UC-L5-4

description: Gene expression data for subject 16, diagnosis UC, layer 5, replicate 2


title: CD43neg D5.P3

description: 1 cell


title: CD43neg D5.P1

description: 1 cell


title: CD43neg D4.P4

description: 1 cell


title: 35-BP-L3-1

description: Gene expression data for subject 35, diagnosis BP, layer 3, replicate 1

value: Bipolar NOS


title: 70-SZ-L5-4

description: Gene expression data for subject 70, diagnosis SZ, layer 5, replicate 2

value: US; AAC


title: 54-MDD-L5-3

description: Gene expression data for subject 54, diagnosis MDD, layer 5, replicate 1


title: CD43neg D4.P2

description: 1 cell


title: 35-BP-L3-2

description: Gene expression data for subject 35, diagnosis BP, layer 3, replicate 2

value: Bipolar


title: 70-SZ-L3-1

description: Gene expression data for subject 70, diagnosis SZ, layer 3, replicate 1

value: Schizophrenia


title: 35-BP-L5-4

description: Gene expression data for subject 35, diagnosis BP, layer 5, replicate 2


title: 54-MDD-L3-1

description: Gene expression data for subject 54, diagnosis MDD, layer 3, replicate 1


title: CIT exposure to Bovine macrophages at 6h_trial#1

description: Gene expression data from bovine macrophage cell line exposed to CIT for 6 hours from trial#1.

value: exposed to CIT for 6 hours


title: 53-MDD-L5-4

description: Gene expression data for subject 53, diagnosis MDD, layer 5, replicate 2

value: Major Depressive Disorder

value: MDD, recurrent


title: CD43neg D5.P0

description: 1 cell


title: 35-BP-L5-3

description: Gene expression data for subject 35, diagnosis BP, layer 5, replicate 1


title: 15-UC-L3-2

description: Gene expression data for subject 15, diagnosis UC, layer 3, replicate 2


title: 70-SZ-L5-3

description: Gene expression data for subject 70, diagnosis SZ, layer 5, replicate 1


title: 16-UC-L3-1

description: Gene expression data for subject 16, diagnosis UC, layer 3, replicate 1


title: 53-MDD-L5-3

description: Gene expression data for subject 53, diagnosis MDD, layer 5, replicate 1


title: 15-UC-L3-1

description: Gene expression data for subject 15, diagnosis UC, layer 3, replicate 1


title: 53-MDD-L3-2

description: Gene expression data for subject 53, diagnosis MDD, layer 3, replicate 2


title: 15-UC-L5-4

description: Gene expression data for subject 15, diagnosis UC, layer 5, replicate 2


title: CD43neg D3.P2

description: 1 cell


title: CD43neg D3.P4

description: 1 cell


title: 69-SZ-L5-4

description: Gene expression data for subject 69, diagnosis SZ, layer 5, replicate 2

value: US; ADR


title: CD43neg D4.P0

description: 1 cell


title: 70-SZ-L3-2

description: Gene expression data for subject 70, diagnosis SZ, layer 3, replicate 2


title: CD43neg D2.P3

description: 1 cell


title: 53-MDD-L3-1

description: Gene expression data for subject 53, diagnosis MDD, layer 3, replicate 1


title: CD43neg D3.P1

description: 1 cell


title: CD43neg D3.P3

description: 1 cell


title: CD43neg D4.P1

description: 1 cell


title: 34-BP-L3-1

description: Gene expression data for subject 34, diagnosis BP, layer 3, replicate 1

value: Bipolar I, PF; ODC; OAR


title: 52-MDD-L5-4

description: Gene expression data for subject 52, diagnosis MDD, layer 5, replicate 2

value: dorsolateral prefrontal cortex

value: MDD; AAR


title: 34-BP-L5-4

description: Gene expression data for subject 34, diagnosis BP, layer 5, replicate 2


title: 34-BP-L5-3

description: Gene expression data for subject 34, diagnosis BP, layer 5, replicate 1


title: PyMT;Lys Cre;E2F3f/f (experimental) H

city: Columbus

first: Prashant

last: Trikha

address: 410 W 12 the Av

institute: Ohio State University

hyb_protocol: Following fragmentation,0.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430.2 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Gene Chips were scanned using the Affy GeneChip Scanner 3000.

data_processing: The data were analyzed with RMAExpress (version 1.0 beta 4) and normalized using Quantile Normalization. Robust mean analysis (RMA) was performed with default parameter settings and the output was log transformed.

source_name: PyMT;Lys Cre;E2F3f/f_F 4/80+ TAMs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA.

tag: strain background

value: FVB

tag: genotype/variation

value: PyMT;Lys Cre:E2f3 f/f

value: mammary tumors

value: F4/80+ FACS sorted tumor-associated macrophages (TAMs)


title: PyMT;Lys Cre;E2F3f/f (experimental) F


title: CD43neg D3.P0

description: 1 cell

value: human iPS-derived CD34+

value: negative


title: 52-MDD-L3-1

description: Gene expression data for subject 52, diagnosis MDD, layer 3, replicate 1

value: pyramidal neuron cell

value: characteristic triangular shape and prominent apical dendrite


title: 34-BP-L3-2

description: Gene expression data for subject 34, diagnosis BP, layer 3, replicate 2

value: Bipolar


title: 15-UC-L5-3

description: Gene expression data for subject 15, diagnosis UC, layer 5, replicate 1

value: Unaffected Comparison subject

value: Unaffected Comparison


title: CD43neg D2.P4

description: 1 cell


title: PyMT;Lys Cre;E2F3f/f (experimental) E


title: 69-SZ-L5-3

description: Gene expression data for subject 69, diagnosis SZ, layer 5, replicate 1

value: Schizophrenia


title: CD43neg D2.P1

description: 1 cell


title: 69-SZ-L3-1

description: Gene expression data for subject 69, diagnosis SZ, layer 3, replicate 1


title: 52-MDD-L5-3

description: Gene expression data for subject 52, diagnosis MDD, layer 5, replicate 1

value: Major Depressive Disorder


title: 69-SZ-L3-2

description: Gene expression data for subject 69, diagnosis SZ, layer 3, replicate 2

value: US; ADR


title: 14-UC-L3-2

description: Gene expression data for subject 14, diagnosis UC, layer 3, replicate 2


title: 33-BP-L5-4

description: Gene expression data for subject 33, diagnosis BP, layer 5, replicate 2

value: Bipolar I; ADC; OAC


title: 33-BP-L5-3

description: Gene expression data for subject 33, diagnosis BP, layer 5, replicate 1

value: dorsolateral prefrontal cortex


title: CD43neg D12.P3

description: 1 cell


title: 14-UC-L5-4

description: Gene expression data for subject 14, diagnosis UC, layer 5, replicate 2


title: 14-UC-L5-3

description: Gene expression data for subject 14, diagnosis UC, layer 5, replicate 1


title: CD43neg D2.P2

description: 1 cell


title: CD43neg D12.P2

description: 1 cell


title: CD43neg D12.P1

description: 1 cell


title: CD43neg D2.P0

description: 1 cell


title: 52-MDD-L3-2

description: Gene expression data for subject 52, diagnosis MDD, layer 3, replicate 2

value: MDD; AAR


title: 68-SZ-L5-3

description: Gene expression data for subject 68, diagnosis SZ, layer 5, replicate 1

value: DS


title: 68-SZ-L3-2

description: Gene expression data for subject 68, diagnosis SZ, layer 3, replicate 2


title: 14-UC-L3-1

description: Gene expression data for subject 14, diagnosis UC, layer 3, replicate 1


title: PyMT;E2F3f/f (control) B

description: A.CEL

source_name: PyMT;E2F3f/f_F 4/80+ TAMs

value: FVB

value: PyMT;E2f3 f/f


title: CD43neg D12.P4

description: 1 cell


title: CD43neg D12.P0

description: 1 cell


title: 51-MDD-L5-4

description: Gene expression data for subject 51, diagnosis MDD, layer 5, replicate 2

value: MDD, recurrent, PF; AAC; ODC


title: 33-BP-L3-1

description: Gene expression data for subject 33, diagnosis BP, layer 3, replicate 1


title: CD43neg D11.P2

description: 1 cell

value: human iPS-derived CD34+


title: 51-MDD-L3-1

description: Gene expression data for subject 51, diagnosis MDD, layer 3, replicate 1


title: PyMT;E2F3f/f (control) D

value: mammary tumors

value: F4/80+ FACS sorted tumor-associated macrophages (TAMs)


title: CD43neg D11.P4

description: 1 cell

value: negative


title: 68-SZ-L5-4

description: Gene expression data for subject 68, diagnosis SZ, layer 5, replicate 2

value: pyramidal neuron cell

value: characteristic triangular shape and prominent apical dendrite


title: PyMT;E2F3f/f (control) G


title: 13-UC-L5-4

description: Gene expression data for subject 13, diagnosis UC, layer 5, replicate 2

value: Unaffected Comparison subject

value: Unaffected Comparison


title: CD43neg D11.P1

description: 1 cell


title: PyMT;Lys Cre;E2F3f/f (experimental) A

value: PyMT;Lys Cre:E2f3 f/f


title: 13-UC-L3-2

description: Gene expression data for subject 13, diagnosis UC, layer 3, replicate 2


title: PyMT;E2F3f/f (control) C


title: CD43neg D11.P0

description: 1 cell


title: CD43neg D11.P3

description: 1 cell


title: 68-SZ-L3-1

description: Gene expression data for subject 68, diagnosis SZ, layer 3, replicate 1

value: Schizophrenia


title: CD43neg D10.P4

description: 1 cell


title: 51-MDD-L5-3

description: Gene expression data for subject 51, diagnosis MDD, layer 5, replicate 1

value: Major Depressive Disorder


title: 33-BP-L3-2

description: Gene expression data for subject 33, diagnosis BP, layer 3, replicate 2

value: dorsolateral prefrontal cortex

value: Bipolar

value: Bipolar I; ADC; OAC


title: 51-MDD-L3-2

description: Gene expression data for subject 51, diagnosis MDD, layer 3, replicate 2


title: 32-BP-L3-2

description: Gene expression data for subject 32, diagnosis BP, layer 3, replicate 2

value: Bipolar I, PF; ADR


title: 13-UC-L3-1

description: Gene expression data for subject 13, diagnosis UC, layer 3, replicate 1


title: CD43neg D10.P3

description: 1 cell


title: 67-SZ-L3-1

description: Gene expression data for subject 67, diagnosis SZ, layer 3, replicate 1

value: DS


title: 13-UC-L5-3

description: Gene expression data for subject 13, diagnosis UC, layer 5, replicate 1


title: 67-SZ-L5-4

description: Gene expression data for subject 67, diagnosis SZ, layer 5, replicate 2


title: CD43neg D10.P2

description: 1 cell


title: 67-SZ-L5-3

description: Gene expression data for subject 67, diagnosis SZ, layer 5, replicate 1


title: 50-MDD-L3-1

description: Gene expression data for subject 50, diagnosis MDD, layer 3, replicate 1

value: MDD, recurrent


title: 32-BP-L3-1

description: Gene expression data for subject 32, diagnosis BP, layer 3, replicate 1


title: 67-SZ-L3-2

description: Gene expression data for subject 67, diagnosis SZ, layer 3, replicate 2


title: CD43neg D10.P1

description: 1 cell

value: human iPS-derived CD34+


title: 50-MDD-L5-3

description: Gene expression data for subject 50, diagnosis MDD, layer 5, replicate 1


title: 50-MDD-L3-2

description: Gene expression data for subject 50, diagnosis MDD, layer 3, replicate 2


title: CD43neg D10.P0

description: 1 cell


title: 32-BP-L5-3

description: Gene expression data for subject 32, diagnosis BP, layer 5, replicate 1


title: 50-MDD-L5-4

description: Gene expression data for subject 50, diagnosis MDD, layer 5, replicate 2


title: 12-UC-L3-1

description: Gene expression data for subject 12, diagnosis UC, layer 3, replicate 1


title: 12-UC-L5-3

description: Gene expression data for subject 12, diagnosis UC, layer 5, replicate 1


title: 12-UC-L5-4

description: Gene expression data for subject 12, diagnosis UC, layer 5, replicate 2


title: CD43neg C9.P4

description: 1 cell


title: 31-BP-L5-4

description: Gene expression data for subject 31, diagnosis BP, layer 5, replicate 2

value: Bipolar I, PF


title: 12-UC-L3-2

description: Gene expression data for subject 12, diagnosis UC, layer 3, replicate 2


title: CD43neg C9.P2

description: 1 cell


title: CD43neg C9.P3

description: 1 cell


title: CD43neg C9.P1

description: 1 cell


title: 31-BP-L5-3

description: Gene expression data for subject 31, diagnosis BP, layer 5, replicate 1


title: 66-SZ-L5-3

description: Gene expression data for subject 66, diagnosis SZ, layer 5, replicate 1

value: SA; AAR


title: 31-BP-L3-2

description: Gene expression data for subject 31, diagnosis BP, layer 3, replicate 2


title: 31-BP-L3-1

description: Gene expression data for subject 31, diagnosis BP, layer 3, replicate 1


title: 66-SZ-L5-4

description: Gene expression data for subject 66, diagnosis SZ, layer 5, replicate 2


title: 66-SZ-L3-1

description: Gene expression data for subject 66, diagnosis SZ, layer 3, replicate 1


title: 49-MDD-L5-4

description: Gene expression data for subject 49, diagnosis MDD, layer 5, replicate 2


title: 49-MDD-L5-3

description: Gene expression data for subject 49, diagnosis MDD, layer 5, replicate 1


title: CD43neg C8.P3

description: 1 cell

value: negative


title: CD43neg C8.P4

description: 1 cell


title: PCA68

city: Vancouver

first: Elai

last: Davicioni

state: British Columbia

address: 1038 Homer st

institute: GenomeDx Biosciences Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using SCAN software package (Bioconductor)

source_name: primary prostate cancer FFPE tissue sample

label_protocol: RNA was amplified, fragmented and biotinylated using the Ovation FFPE system v 3.0 (NuGEN)

extract_protocol: RNA was extracted using the Qiagen RNeasy FFPE Kit .

value: prostate cancer


title: 66-SZ-L3-2

description: Gene expression data for subject 66, diagnosis SZ, layer 3, replicate 2

value: pyramidal neuron cell

value: characteristic triangular shape and prominent apical dendrite


title: 49-MDD-L3-2

description: Gene expression data for subject 49, diagnosis MDD, layer 3, replicate 2


title: CD43neg C8.P1

description: 1 cell


title: CD43neg C8.P2

description: 1 cell


title: 49-MDD-L3-1

description: Gene expression data for subject 49, diagnosis MDD, layer 3, replicate 1


title: 11-UC-L5-4

description: Gene expression data for subject 11, diagnosis UC, layer 5, replicate 2

value: Unaffected Comparison subject

value: Unaffected Comparison


title: CD43neg C8.P0

description: 1 cell


title: 11-UC-L3-1

description: Gene expression data for subject 11, diagnosis UC, layer 3, replicate 1


title: 11-UC-L5-3

description: Gene expression data for subject 11, diagnosis UC, layer 5, replicate 1


title: 30-BP-L5-3

description: Gene expression data for subject 30, diagnosis BP, layer 5, replicate 1

value: Bipolar I; ODC


title: 11-UC-L3-2

description: Gene expression data for subject 11, diagnosis UC, layer 3, replicate 2


title: 30-BP-L5-4

description: Gene expression data for subject 30, diagnosis BP, layer 5, replicate 2


title: CD43neg C9.P0

description: 1 cell


title: CD43neg C7.P4

description: 1 cell


title: PCA70


title: PCA67


title: PCA65


title: PCA69


title: 30-BP-L3-1

description: Gene expression data for subject 30, diagnosis BP, layer 3, replicate 1


title: 65-SZ-L5-4

description: Gene expression data for subject 65, diagnosis SZ, layer 5, replicate 2

value: Schizophrenia

value: US; ADC; OAC


title: 65-SZ-L5-3

description: Gene expression data for subject 65, diagnosis SZ, layer 5, replicate 1

value: dorsolateral prefrontal cortex


title: CD43neg C7.P1

description: 1 cell


title: 30-BP-L3-2

description: Gene expression data for subject 30, diagnosis BP, layer 3, replicate 2

value: Bipolar


title: CD43neg C7.P2

description: 1 cell


title: 65-SZ-L3-2

description: Gene expression data for subject 65, diagnosis SZ, layer 3, replicate 2


title: 48-MDD-L5-3

description: Gene expression data for subject 48, diagnosis MDD, layer 5, replicate 1

value: Major Depressive Disorder

value: MDD, recurrent; ADR; ODC


title: PCA64


title: 48-MDD-L3-2

description: Gene expression data for subject 48, diagnosis MDD, layer 3, replicate 2


title: 48-MDD-L5-4

description: Gene expression data for subject 48, diagnosis MDD, layer 5, replicate 2


title: CD43neg C6.P4

description: 1 cell


title: PCA59


title: PCA66


title: PCA57


title: PCA63


title: 48-MDD-L3-1

description: Gene expression data for subject 48, diagnosis MDD, layer 3, replicate 1


title: PCA62


title: 10-UC-L5-3

description: Gene expression data for subject 10, diagnosis UC, layer 5, replicate 1


title: CD43neg C7.P3

description: 1 cell


title: 10-UC-L3-2

description: Gene expression data for subject 10, diagnosis UC, layer 3, replicate 2


title: 10-UC-L3-1

description: Gene expression data for subject 10, diagnosis UC, layer 3, replicate 1


title: CD43neg C6.P3

description: 1 cell


title: 29-BP-L5-4

description: Gene expression data for subject 29, diagnosis BP, layer 5, replicate 2

value: Bipolar I, PF; AAR; ODC; OAC


title: PCA56


title: PCA58


title: 65-SZ-L3-1

description: Gene expression data for subject 65, diagnosis SZ, layer 3, replicate 1


title: CD43neg C7.P0

description: 1 cell

value: human iPS-derived CD34+


title: PCA60


title: CD43neg C6.P1

description: 1 cell


title: 64-SZ-L5-3

description: Gene expression data for subject 64, diagnosis SZ, layer 5, replicate 1

value: DS; OAR


title: 29-BP-L3-1

description: Gene expression data for subject 29, diagnosis BP, layer 3, replicate 1


title: CD43neg C6.P2

description: 1 cell


title: PCA61


title: PCA53


title: CD43neg C6.P0

description: 1 cell


title: 64-SZ-L3-2

description: Gene expression data for subject 64, diagnosis SZ, layer 3, replicate 2


title: 29-BP-L5-3

description: Gene expression data for subject 29, diagnosis BP, layer 5, replicate 1


title: CD43neg C5.P4

description: 1 cell


title: 47-MDD-L5-4

description: Gene expression data for subject 47, diagnosis MDD, layer 5, replicate 2

value: MDD


title: 64-SZ-L5-4

description: Gene expression data for subject 64, diagnosis SZ, layer 5, replicate 2


title: 47-MDD-L5-3

description: Gene expression data for subject 47, diagnosis MDD, layer 5, replicate 1


title: CD43neg C5.P3

description: 1 cell

value: negative


title: 47-MDD-L3-2

description: Gene expression data for subject 47, diagnosis MDD, layer 3, replicate 2


title: PCA50

value: prostate cancer


title: CD43neg C5.P2

description: 1 cell


title: 47-MDD-L3-1

description: Gene expression data for subject 47, diagnosis MDD, layer 3, replicate 1

value: pyramidal neuron cell


title: 9-UC-L5-4

description: Gene expression data for subject 9, diagnosis UC, layer 5, replicate 2

value: characteristic triangular shape and prominent apical dendrite


title: PCA54


title: PCA55


title: PCA52


title: 9-UC-L5-3

description: Gene expression data for subject 9, diagnosis UC, layer 5, replicate 1

value: Unaffected Comparison subject


title: CD43neg C5.P1

description: 1 cell


title: 9-UC-L3-1

description: Gene expression data for subject 9, diagnosis UC, layer 3, replicate 1

value: Unaffected Comparison


title: 9-UC-L3-2

description: Gene expression data for subject 9, diagnosis UC, layer 3, replicate 2


title: PCA51


title: PCA49


title: 28-BP-L5-3

description: Gene expression data for subject 28, diagnosis BP, layer 5, replicate 1

value: Bipolar I; AAR


title: 64-SZ-L3-1

description: Gene expression data for subject 64, diagnosis SZ, layer 3, replicate 1

value: Schizophrenia


title: 28-BP-L5-4

description: Gene expression data for subject 28, diagnosis BP, layer 5, replicate 2


title: 46-MDD-L5-4

description: Gene expression data for subject 46, diagnosis MDD, layer 5, replicate 2

value: MDD, PF; AAR


title: CD43neg C5.P0

description: 1 cell


title: PCA47


title: CD43neg C4.P4

description: 1 cell


title: CD43neg C4.P3

description: 1 cell


title: 28-BP-L3-1

description: Gene expression data for subject 28, diagnosis BP, layer 3, replicate 1

value: dorsolateral prefrontal cortex


title: CD43neg C4.P2

description: 1 cell


title: PCA48


title: CD43neg C4.P0

description: 1 cell


title: 8-UC-L5-4

description: Gene expression data for subject 8, diagnosis UC, layer 5, replicate 2


title: 46-MDD-L5-3

description: Gene expression data for subject 46, diagnosis MDD, layer 5, replicate 1


title: 8-UC-L3-2

description: Gene expression data for subject 8, diagnosis UC, layer 3, replicate 2


title: 46-MDD-L3-2

description: Gene expression data for subject 46, diagnosis MDD, layer 3, replicate 2


title: 46-MDD-L3-1

description: Gene expression data for subject 46, diagnosis MDD, layer 3, replicate 1


title: 8-UC-L5-3

description: Gene expression data for subject 8, diagnosis UC, layer 5, replicate 1


title: PCA46


title: PCA44


title: 8-UC-L3-1

description: Gene expression data for subject 8, diagnosis UC, layer 3, replicate 1


title: CD43neg C3.P4

description: 1 cell


title: 28-BP-L3-2

description: Gene expression data for subject 28, diagnosis BP, layer 3, replicate 2

value: Bipolar


title: CD43neg C3.P3

description: 1 cell


title: 27-BP-L5-3

description: Gene expression data for subject 27, diagnosis BP, layer 5, replicate 1

value: Bipolar I, PF


title: PCA45


title: 63-SZ-L5-3

description: Gene expression data for subject 63, diagnosis SZ, layer 5, replicate 1

value: US


title: CD43neg C4.P1

description: 1 cell


title: 27-BP-L3-1

description: Gene expression data for subject 27, diagnosis BP, layer 3, replicate 1


title: PCA41


title: 63-SZ-L3-2

description: Gene expression data for subject 63, diagnosis SZ, layer 3, replicate 2


title: 27-BP-L5-4

description: Gene expression data for subject 27, diagnosis BP, layer 5, replicate 2


title: 63-SZ-L3-1

description: Gene expression data for subject 63, diagnosis SZ, layer 3, replicate 1


title: CD43neg C3.P1

description: 1 cell


title: 45-MDD-L5-4

description: Gene expression data for subject 45, diagnosis MDD, layer 5, replicate 2

value: Major Depressive Disorder

value: MDD, recurrent; ADC


title: CD43neg C3.P2

description: 1 cell

value: human iPS-derived CD34+


title: 45-MDD-L5-3

description: Gene expression data for subject 45, diagnosis MDD, layer 5, replicate 1


title: CD43neg C3.P0

description: 1 cell


title: 45-MDD-L3-2

description: Gene expression data for subject 45, diagnosis MDD, layer 3, replicate 2


title: CD43neg C2.P4

description: 1 cell


title: PCA42


title: CD43neg C2.P3

description: 1 cell


title: 7-UC-L3-1

description: Gene expression data for subject 7, diagnosis UC, layer 3, replicate 1


title: PCA38


title: CD43neg C2.P2

description: 1 cell


title: 7-UC-L5-4

description: Gene expression data for subject 7, diagnosis UC, layer 5, replicate 2


title: PCA39


title: PCA40


title: 7-UC-L3-2

description: Gene expression data for subject 7, diagnosis UC, layer 3, replicate 2


title: 26-BP-L5-3

description: Gene expression data for subject 26, diagnosis BP, layer 5, replicate 1


title: 7-UC-L5-3

description: Gene expression data for subject 7, diagnosis UC, layer 5, replicate 1


title: 26-BP-L5-4

description: Gene expression data for subject 26, diagnosis BP, layer 5, replicate 2


title: CD43neg C2.P1

description: 1 cell


title: PCA43


title: 45-MDD-L3-1

description: Gene expression data for subject 45, diagnosis MDD, layer 3, replicate 1


title: 26-BP-L3-2

description: Gene expression data for subject 26, diagnosis BP, layer 3, replicate 2


title: CD43neg C2.P0

description: 1 cell


title: 26-BP-L3-1

description: Gene expression data for subject 26, diagnosis BP, layer 3, replicate 1


title: PCA34


title: PCA36


title: CD43neg C12.P4

description: 1 cell


title: 62-SZ-L5-3

description: Gene expression data for subject 62, diagnosis SZ, layer 5, replicate 1

value: US; AAR; OAR


title: 62-SZ-L3-1

description: Gene expression data for subject 62, diagnosis SZ, layer 3, replicate 1


title: PCA33


title: 62-SZ-L3-2

description: Gene expression data for subject 62, diagnosis SZ, layer 3, replicate 2


title: CD43neg C12.P3

description: 1 cell

value: negative


title: 62-SZ-L5-4

description: Gene expression data for subject 62, diagnosis SZ, layer 5, replicate 2


title: 44-MDD-L5-3

description: Gene expression data for subject 44, diagnosis MDD, layer 5, replicate 1

value: MDD, PF


title: 44-MDD-L5-4

description: Gene expression data for subject 44, diagnosis MDD, layer 5, replicate 2

value: pyramidal neuron cell


title: PCA37

value: prostate cancer


title: PCA30


title: 6-UC-L5-3

description: Gene expression data for subject 6, diagnosis UC, layer 5, replicate 1

value: characteristic triangular shape and prominent apical dendrite

value: Unaffected Comparison subject


title: 6-UC-L5-4

description: Gene expression data for subject 6, diagnosis UC, layer 5, replicate 2

value: Unaffected Comparison


title: PCA35


title: 44-MDD-L3-2

description: Gene expression data for subject 44, diagnosis MDD, layer 3, replicate 2


title: CD43neg C12.P1

description: 1 cell


title: 44-MDD-L3-1

description: Gene expression data for subject 44, diagnosis MDD, layer 3, replicate 1


title: CD43neg C12.P2

description: 1 cell


title: 6-UC-L3-1

description: Gene expression data for subject 6, diagnosis UC, layer 3, replicate 1


title: CD43neg C12.P0

description: 1 cell


title: 25-BP-L5-4

description: Gene expression data for subject 25, diagnosis BP, layer 5, replicate 2

value: Bipolar I, PF; AAR


title: 6-UC-L3-2

description: Gene expression data for subject 6, diagnosis UC, layer 3, replicate 2


title: PCA31


title: CD43neg C11.P4

description: 1 cell


title: 25-BP-L5-3

description: Gene expression data for subject 25, diagnosis BP, layer 5, replicate 1


title: CD43neg C11.P3

description: 1 cell


title: 25-BP-L3-1

description: Gene expression data for subject 25, diagnosis BP, layer 3, replicate 1


title: 25-BP-L3-2

description: Gene expression data for subject 25, diagnosis BP, layer 3, replicate 2


title: 43-MDD-L5-3

description: Gene expression data for subject 43, diagnosis MDD, layer 5, replicate 1

value: MDD; ADR