title: 669 - mAdbID:66148

description: mAdb experiment ID: 66148

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:7.11

value: LDH ratio:0.68


title: 424 - mAdbID:66181

status: Public on Sep 04 2008

type: RNA

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

country: USA

institute: National Cancer Institute

description: mAdb experiment ID: 66181

hyb_protocol: Affymetrix Hybridization Protocol Other: Following fragmentation, 11 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affy Scanning Protocol Other: Scanning was performed by the Affymetrix 3000 Scanner.

data_processing:
MAS 5.0 Data Processing Protocol
Calculation Method: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was extracted using All Prep RNA/DNA kit (Qiagen, Valencia, CA) according to the manufacturers' protocols.

tag: Gender

value: female

tag: Age

tag: Tissue

value: lymph node

tag: Disease state

value: Lymphoma

tag: Individual

tag: Clinical info

value: Submitting diagnosis:DLBCL

value: Follow up status:DEAD

value: Follow up years:10.62

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:3

value: LDH ratio:1.54

value: Number of extranodal sites:1


title: 687 - mAdbID:66150

description: mAdb experiment ID: 66150

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.94

value: ECOG performance status:1

value: LDH ratio:3.99

value: Number of extranodal sites:0


title: 1005 - mAdbID:66132

description: mAdb experiment ID: 66132

value: male

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:5.77

value: LDH ratio:0.61


title: 874 - mAdbID:66155

description: mAdb experiment ID: 66155

value: lymph node

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:0.12

value: LDH ratio:1.1


title: 810 - mAdbID:66151

description: mAdb experiment ID: 66151

value: female

value: Follow up years:11.72

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:0

value: LDH ratio:0.56


title: 668 - mAdbID:66147

description: mAdb experiment ID: 66147

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:6.44

value: ECOG performance status:1

value: LDH ratio:1.68


title: 1049 - mAdbID:66116

description: mAdb experiment ID: 66116

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:DEAD

value: Follow up years:1.33

value: LDH ratio:1.56

value: Number of extranodal sites:1


title: 432 - mAdbID:66183

description: mAdb experiment ID: 66183

value: male

value: lymph node

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:0.38

value: LDH ratio:NA

value: Number of extranodal sites:0


title: 860 - mAdbID:66152

description: mAdb experiment ID: 66152

value: female

value: Follow up years:3.03

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:0

value: LDH ratio:0.77


title: 809 - mAdbID:66156

description: mAdb experiment ID: 66156

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.51

value: LDH ratio:1.31


title: 1008 - mAdbID:66133

description: mAdb experiment ID: 66133

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:6.46

value: ECOG performance status:1

value: LDH ratio:0.48


title: 434 - mAdbID:66103

description: mAdb experiment ID: 66103

value: lymph node

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:10.53


title: 538 - mAdbID:66101

description: mAdb experiment ID: 66101

value: female

value: Follow up status:DEAD

value: Follow up years:0.34

value: ECOG performance status:3

value: LDH ratio:NA

value: Number of extranodal sites:1


title: 529 - mAdbID:66144

description: mAdb experiment ID: 66144

value: male

value: Follow up years:1.06

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:1.37


title: 1039 - mAdbID:66113

description: mAdb experiment ID: 66113

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:2.05

value: ECOG performance status:2

value: Number of extranodal sites:0


title: 807 - mAdbID:66154

description: mAdb experiment ID: 66154

value: lymph node

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.31

value: ECOG performance status:1

value: LDH ratio:1.22


title: 672 - mAdbID:66149

description: mAdb experiment ID: 66149

value: female

value: Submitting diagnosis:DLBCL

value: Follow up status:ALIVE

value: Follow up years:6.78

value: LDH ratio:0.49


title: 492 - mAdbID:66106

description: mAdb experiment ID: 66106

value: male

value: Follow up years:11.29

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:0


title: 459 - mAdbID:66104

description: mAdb experiment ID: 66104

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:9.65

value: ECOG performance status:2


title: 663 - mAdbID:66146

description: mAdb experiment ID: 66146

value: lymph node

value: Lymphoma

value: Follow up status:DEAD

value: Follow up years:0.62

value: LDH ratio:0.99

value: Number of extranodal sites:0


title: 470 - mAdbID:66105

description: mAdb experiment ID: 66105

value: Submitting diagnosis:DLBCL

value: Follow up years:11.17

value: LDH ratio:2.09


title: 1043 - mAdbID:66114

description: mAdb experiment ID: 66114

value: female

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:2.31


title: 1045 - mAdbID:66115

description: mAdb experiment ID: 66115

value: male

value: Follow up years:2.26

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:0.98

value: Number of extranodal sites:1


title: 617 - mAdbID:66102

description: mAdb experiment ID: 66102

value: lymph node

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:5.88

value: ECOG performance status:0

value: LDH ratio:0.61


title: 415 - mAdbID:66100

description: mAdb experiment ID: 66100

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up status:DEAD

value: Follow up years:5.38

value: LDH ratio:1.21

value: Number of extranodal sites:0


title: 1037 - mAdbID:66072

description: mAdb experiment ID: 66072

value: female

value: Follow up years:0.23

value: ECOG performance status:3


title: 1038 - mAdbID:66073

description: mAdb experiment ID: 66073

value: male

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.71

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1


title: 481 - mAdbID:66229

description: mAdb experiment ID: 66229

value: lymph node

value: Follow up status:ALIVE

value: Follow up years:10.75

value: ECOG performance status:2

value: LDH ratio:0.82

value: Number of extranodal sites:1


title: 1021 - mAdbID:66064

description: mAdb experiment ID: 66064

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:14.59

value: LDH ratio:2.15


title: 1034 - mAdbID:66071

description: mAdb experiment ID: 66071

value: female

value: Follow up status:DEAD

value: Follow up years:2.31

value: ECOG performance status:0

value: Number of extranodal sites:0


title: 744 - mAdbID:65821

description: mAdb experiment ID: 65821

value: Follow up years:8.86

value: Chemotherapy:CHOP-Like Regimen


title: 1031 - mAdbID:66070

description: mAdb experiment ID: 66070

value: male

value: lymph node

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:6.64


title: 1027 - mAdbID:66069

description: mAdb experiment ID: 66069

value: Follow up years:0.25

value: ECOG performance status:2


title: 872 - mAdbID:66062

description: mAdb experiment ID: 66062

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up status:ALIVE

value: Follow up years:5

value: ECOG performance status:1

value: LDH ratio:1.7


title: 701 - mAdbID:66061

description: mAdb experiment ID: 66061

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:3.9

value: LDH ratio:1.54


title: 1026 - mAdbID:66068

description: mAdb experiment ID: 66068

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:DEAD

value: Follow up years:6.94

value: Number of extranodal sites:0


title: 1023 - mAdbID:66065

description: mAdb experiment ID: 66065

value: female

value: lymph node

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:5.57

value: Chemotherapy:CHOP-Like Regimen


title: 572 - mAdbID:65819

description: mAdb experiment ID: 65819

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:14.24

value: ECOG performance status:0

value: LDH ratio:0.88


title: 695 - mAdbID:65827

description: mAdb experiment ID: 65827

value: male

value: Follow up years:0.15

value: ECOG performance status:1

value: LDH ratio:0.77


title: 742 - mAdbID:65816

description: mAdb experiment ID: 65816

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:4.09

value: LDH ratio:0.5


title: 565 - mAdbID:65817

description: mAdb experiment ID: 65817

value: lymph node

value: Follow up status:DEAD

value: Follow up years:9.11

value: LDH ratio:1.15

value: Number of extranodal sites:0


title: 688 - mAdbID:65818

description: mAdb experiment ID: 65818

value: female

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:0.33

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:0.78


title: 674 - mAdbID:65815

description: mAdb experiment ID: 65815

value: Follow up years:7.22

value: ECOG performance status:1

value: LDH ratio:0.775


title: 547 - mAdbID:65798

description: mAdb experiment ID: 65798

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.05

value: LDH ratio:NA

value: Number of extranodal sites:1


title: 756 - mAdbID:65797

description: mAdb experiment ID: 65797

value: male

value: lymph node

value: Follow up status:ALIVE

value: Follow up years:7.21

value: ECOG performance status:0


title: 694 - mAdbID:65796

description: mAdb experiment ID: 65796

value: Lymphoma

value: Follow up years:4.83

value: LDH ratio:0.68

value: Number of extranodal sites:0


title: 841 - mAdbID:65799

description: mAdb experiment ID: 65799

value: Submitting diagnosis:DLBCL

value: Follow up years:10.14

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:2.56


title: 711 - mAdbID:65824

description: mAdb experiment ID: 65824

value: female

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:DEAD

value: Follow up years:3.93

value: ECOG performance status:3

value: LDH ratio:0.4


title: 747 - mAdbID:65802

description: mAdb experiment ID: 65802

value: male

value: lymph node

value: Follow up status:ALIVE

value: Follow up years:15.41

value: ECOG performance status:1

value: LDH ratio:NA


title: 689 - mAdbID:65794

description: mAdb experiment ID: 65794

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:2.54

value: LDH ratio:1.01

value: Number of extranodal sites:0


title: 704 - mAdbID:65795

description: mAdb experiment ID: 65795

value: female

value: Submitting diagnosis:DLBCL

value: Follow up years:9.67

value: Chemotherapy:CHOP-Like Regimen


title: 553 - mAdbID:65793

description: mAdb experiment ID: 65793

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:DEAD

value: Follow up years:0.82

value: ECOG performance status:0

value: LDH ratio:1.12


title: 549 - mAdbID:65792

description: mAdb experiment ID: 65792

value: male

value: lymph node

value: Follow up years:2.68


title: Crtc1 WT

city: San Diego

first: Marc

last: Montminy

state: CA

address: 10010 N. Torrey Pines Rd

department: PBL

institute: Salk Institute

description: gene expression data from wild-type hypothalami following 6h of refeeding

hyb_protocol: Following fragmentation, 30ug of cRNA was hybridized to the affymetrix mouse genome 430 2.0 array

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating Software using default settings.

organism: Mus musculus

source_name: Crtc1 wild-type hypothalamus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 30 ug total RNA

growth_protocol: 12-week old male mice

extract_protocol: Trizol extraction followed by DNAse treatment and post-clean up with Qiagen Rneasy columns

treatment_protocol: Mice were fasted overnight for 18h and refed for 6h

tag: 6h of refeeding, 12-week old mice


title: RCC399_normal tissue

status: Public on Sep 03 2008

city: Tuebingen

first: Andreas

middle: Oliver

last: Weinzierl

address: Auf der Morgenstelle 15

department: Department of Immunology

country: Germany

institute: University of Tuebingen

description: HLA typing: A*01, A*02, B*08, B*50, DRB1*03, DRB3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. Incubation, washing, and staining were carried out according to the GeneChip Mapping Assay Manual, using standard protocols on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene-Chip Scanner 3000.

data_processing: Data were analyzed with the GCOS software (Affymetrix), using default settings for all parameters. Pairwise comparisons were calculated using the respective normal kidney array as baseline. For normalization, 100 housekeeping genes provided by Affymetrix were used (http://www.affymetrix.com/support/technical/mask_files.affx). Relative expression values were calculated from the signal log ratios given by the software.

source_name: normal kidney tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary human tissue.

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

treatment_protocol: Tissues were shock-frozen in liquid nitrogen directly after surgery.

tag: Date of birth


title: RCC399_tumor tissue

source_name: clear cell renal cell carcinoma


title: RCC377_tumor tissue

description: HLA typing: A*01, A*03, B*07, DRB1*03, DRB1*11, DRB3


title: RCC343_metastatic tissue

description: HLA typing: A*01, A*31, B*08, B*15, DRB1*03, DRB1*04, DRB3, DRB4

source_name: metastasis clear cell renal cell carcinoma


title: RCC343_tumor tissue


title: Crtc1 KO

description: gene expression data from Crtc1 knockout hypothalami following 6h of refeeding

data_processing: The data were analyzed with the Affymetrix GeneChip Operating Software using default settings

source_name: Crtc1 knockout hypothalamus


title: RCC377_normal tissue


title: RCC377_metastatic tissue


title: kidney_normal tissue

description: Purchased from Clontech.

source_name: pooled normal kidney tissue

tag: 12 kidneys pooled


title: RCC399_metastatic tissue


title: RCC343_normal tissue


title: root - 21% oxygen - 48h - B

status: Public on Sep 01 2008

city: Potsdam

first: Joost

middle: T.

last: van Dongen

address: Am Muehlenberg 1

institute: Max Planck Institute of Molecular Plant Physiology

description: roots of 2 weeks old seedlings grown on vertical agar plates

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

organism: Arabidopsis thaliana

source_name: root

label_protocol: 10ug of total RNA was biotin labelled

growth_protocol: Arabidopsis thaliana ecotype col2 seedlings were grown in a 12h light / 12 h dark cycle (day and night temperature was 22°C) on vertical agar plates supplemented with half-strength Murashige and Skoog (MS) medium (Duchefa Biochemie B.V., Haarlem, the Netherlands) supplemented with 1% sucrose. The roots of the plants were growing on the surface of the agar, thus avoiding restricted oxygen diffusion towards the roots by the agar medium.

extract_protocol: Trizol, according to the protocol recommended by the supplier (GibcoBRL Life Technologies)

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 21% oxygen , 350 ppm CO2, and N2 (control) was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 48 hours of each oxygen treatment.

tag: ecotype col2


title: root - 08% oxygen - 48h - B

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 8% oxygen , 350 ppm CO2, and N2 (control) was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 48 hours of each oxygen treatment.

tag: ecotypte col2


title: root - 21% oxygen - 30min - G

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 21% oxygen , 350 ppm CO2, and N2 (control) was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 30 min of each oxygen treatment.


title: root - 21% oxygen - 30min - F


title: root - 21% oxygen - 48h - F


title: root - 21% oxygen - 48h - A


title: root - 21% oxygen - 2h - E

growth_protocol: Arabidopsis thaliana ecotype col2 seedlings were grown in a 12h light / 12 h dark cycle (day and night temperature was 22Â°C) on vertical agar plates supplemented with half-strength Murashige and Skoog (MS) medium (Duchefa Biochemie B.V., Haarlem, the Netherlands) supplemented with 1% sucrose. The roots of the plants were growing on the surface of the agar, thus avoiding restricted oxygen diffusion towards the roots by the agar medium.

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 21% oxygen , 350 ppm CO2, and N2 (control) was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 2 hours of each oxygen treatment.


title: root - 21% oxygen - 30min - C


title: root - 08% oxygen - 2h - C

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 8% oxygen , 350 ppm CO2, and N2 was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 2 hours of each oxygen treatment.


title: root - 21% oxygen - 2h - D

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 21% oxygen , 350 ppm CO2, and N2 was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 2 hours of each oxygen treatment.


title: root - 08% oxygen - 30min - G

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 8% oxygen , 350 ppm CO2, and N2 was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 30 minutes of each oxygen treatment.


title: root - 08% oxygen - 48h - F

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 8% oxygen , 350 ppm CO2, and N2 was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 48 hours of each oxygen treatment.


title: root - 08% oxygen - 2h - F


title: root - 04% oxygen - 30min - F

extract_protocol: Trizol, according to the protocol recommended by the supplier (GibcoBRL Life Technologies

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 4% oxygen concentrations, 350 ppm CO2, and N2 was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 30 min. of each oxygen treatment.


title: root - 04% oxygen - 30min - D

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 4% oxygen concentrations, 350 ppm CO2, and N2 was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 30 min of each oxygen treatment.


title: WT leaf-drought-rep3

city: Raleigh

first: Imara

last: Perera

state: NC

address: Campus Box 7612

department: Plant Biology

institute: North Carolina State University

description: WT leaf-drought-rep3

hyb_protocol: Arabidopsis arrays (ATH1 from Affymetrix Inc) were hybridized using the Affymetrix fluidics station.

scan_protocol: Data acquisition and analysis was carried out by Expression Analysis Inc. (Durham, NC) using the Affymetrix scanner and GCOS software.

data_processing: An estimate of signal for each transcript was calculated based on the Microarray Suite 5.0 algorithm (Affymetrix) and raw fold-change for each transcript was calculated by taking the simple ratio of the geometric means of the signal values for each respective group.

source_name: wild type (WT) leaf, drought, replicate 3

label_protocol: Biotinylated target cRNA was synthesized using the Two cycle Target Labeling protocol (Affymetrix Inc, Santa Clara, CA).

growth_protocol: Wild type (Col 0) and InsP 5-ptase transgenic Arabidopsis plants were grown in the NC State University Phytotron in a growth chamber, under short day conditions (8h light/16 dark) at 21C with a light intensity of ~ 150 μmol m-2 sec-1.

extract_protocol: RNA was isolated using the Plant RNeasy kit (Qiagen, Valencia, CA).

treatment_protocol: Leaf samples (pooled from 10 plants/line) were collected on day 0 and day 7 of the RWC time course and frozen immediately in liquid N2.

tag: fully expanded leaves- 7d without water

tag: 8 week old plants


title: T8 leaf-drought-rep2

description: T8 leaf-drought-rep2

source_name: transgenic line (T8) leaf, drought, replicate 2


title: root - 21% oxygen - 2h - F


title: root - 08% oxygen - 30min - C


title: C2 leaf-drought-rep2

description: C2 leaf-drought-rep2

source_name: control line (C2) leaf, drought, replicate 2


title: root - 04% oxygen - 48h - F

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 4% oxygen, 350 ppm CO2, and N2 was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 48 hours of each oxygen treatment.


title: T6 leaf-drought-rep3

description: T6 leaf-drought-rep3

source_name: transgenic line (T6) leaf, drought, replicate 3


title: C2 leaf-well watered-rep2

description: C2 leaf-well watered-rep2

source_name: control line (C2) leaf, well watered, replicate 2

tag: fully expanded leaves- well watered


title: T8 leaf-drought-rep3

description: T8 leaf-drought-rep3

source_name: transgenic line (T8) leaf, drought, replicate 3


title: root - 04% oxygen - 48h - B

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 4% oxygen concentrations, 350 ppm CO2, and N2 was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 48 hours of each oxygen treatment.


title: T8 leaf-well watered-rep3

description: T8 leaf-well watered-rep3

source_name: transgenic line (T8) leaf, well watered, replicate 3


title: root - 04% oxygen - 2h - F

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 4% oxygen concentrations, 350 ppm CO2, and N2 was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 2 hours of each oxygen treatment.


title: WT leaf-well watered-rep3

description: WT leaf-well watered-rep3

source_name: wild type (WT) leaf, well watered, replicate 3


title: root - 08% oxygen - 48h - A


title: root - 01% oxygen - 48h - A

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 1% oxygen concentrations, 350 ppm CO2, and N2 was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 48 hours of each oxygen treatment.


title: T8 leaf-well watered-rep2

description: T8 leaf-well watered-rep2

source_name: transgenic line (T8) leaf, well watered, replicate 2


title: root - 01% oxygen - 48h - F


title: root - 01% oxygen - 30min - F

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 1% oxygen concentrations, 350 ppm CO2, and N2 was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 30min of each oxygen treatment.


title: root - 01% oxygen - 30min - D

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 1% oxygen concentrations, 350 ppm CO2, and N2 was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 30 min of each oxygen treatment.


title: root - 01% oxygen - 2h - F

treatment_protocol: Ten days after germination, seedlings were transferred to continuous darkness and a stream of premixed air containing 1% oxygen concentrations, 350 ppm CO2, and N2 was blown over the plates. Oxygen concentrations within the plates were regularly controlled to ensure precise regulation of the actual oxygen concentration around the roots. Roots were harvested in liquid nitrogen after 2 hours of each oxygen treatment.


title: root - 01% oxygen - 2h - E


title: T6 leaf-drought-rep2

description: T6 leaf-drought-rep2

source_name: transgenic line (T6) leaf, drought, replicate 2


title: WT leaf-well watered-rep2

description: WT leaf-well watered-rep2

source_name: wild type (WT) leaf, well watered, replicate 2


title: WT leaf-drought-rep2

description: WT leaf-drought-rep2

source_name: wild type (WT) leaf, drought, replicate 2


title: T6 leaf-well watered-rep3

description: T6 leaf-well watered-rep3

source_name: transgenic line (T6) leaf, well watered, replicate 3


title: T6 leaf-well watered-rep2

description: T6 leaf-well watered-rep2

source_name: transgenic line (T6) leaf, well watered, replicate 2


title: C2 leaf-well watered-rep1

description: C2 leaf-well watered-rep1

source_name: control line (C2) leaf, well watered, replicate 1


title: T6 leaf-drought-rep1

description: T6 leaf-drought-rep1

source_name: transgenic line (T6) leaf, drought, replicate 1


title: C2 leaf-drought-rep1

description: C2 leaf-drought-rep1

source_name: control line (C2) leaf, drought, replicate 1


title: root - 04% oxygen - 2h - D

source_name: root


title: T8 leaf-drought-rep1

description: T8 leaf-drought-rep1

source_name: transgenic line (T8) leaf, drought, replicate 1


title: WT leaf-well watered-rep1

description: WT leaf-well watered-rep1

source_name: wild type (WT) leaf, well watered, replicate 1


title: WT leaf-drought-rep1

description: WT leaf-drought-rep1

source_name: wild type (WT) leaf, drought, replicate 1


title: T8 leaf-well watered-rep1

description: T8 leaf-well watered-rep1

source_name: transgenic line (T8) leaf, well watered, replicate 1


title: Phloem exudate_1

city: Wuerzburg

first: Rosalia

last: Deeken

address: Julius-von-Sachs-Platz 2

department: Department of Molecular Plant Physiology and Biophysics

institute: University of Wuerzburg, Julius-von-Sachs-Institute

description: Microarray analysis were conducted at The Microarray Facility, University of Tuebingen, Germany. RNA of the sample was subjected to two rounds of linear amplification using the Affymetrix “Two-Cycle cDNA synthesis kit” (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions.

hyb_protocol: Affymetrix protocol.

scan_protocol: Microarrays were scanned using the GCS3000 Gene Chip scanner (Affymetrix) and GCOS 1.4 software.

data_processing: Affymetrix MAS 5.0 software.

molecule: polyA RNA

source_name: Phloem exudate of Arabidopsis

label_protocol: Affymetrix protocol.

growth_protocol: Plants were cultivated under short day conditions (8 h light, 22 °C / 16 h darkness, 16 °C) in a growth chamber (Percival Scientific, Inc. USA).

extract_protocol: PolyA-RNA was extracted from phloem exudates using Oligo-dT25 Dynabeads (Dynal, Hamburg, Germany) according to the manufacturer’s protocol.

tag: Phloem exudate of adult leaves of early flowering Arabidopsis thaliana, ecotype Col-0 extracted by the EDTA-chelation technique.


title: Phloem exudate_3

description: Microarray analysis were conducted at The Microarray Facility, University of Tuebingen Germany. RNA of the sample was subjected to two rounds of linear amplification using Affymetrix “Two-Cycle cDNA synthesis kit” (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions.

growth_protocol: Plants were cultivated under short day conditions (8 h light, 22 °C / 16 h darkness, 16°C) in a growth chamber (Percival Scientific, Inc. USA).


title: Noninjured eye 2

city: Chicago

first: Thomas

middle: J

last: Lukas

state: IL

address: 303 E. Chicago Ave

department: MPBC

institute: Northwestern University

description: Control 2

hyb_protocol: Labeled cRNA (8 Âµg) was subjected to in invitro transcription and hybridized to Affymetrix (Santa Clara, CA) Mu430 v2.0 chips as recommended by the manufacturer. Chips were hybridized for 16 hr at 45 deg in an Affymetrix 640 hybridization oven.

scan_protocol: Preparation of microarrays for scanning was carried out with Affymetrix wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.

data_processing: For each dataset, invariant set normalization was performed using the PM/MM model for calculating signal intensities in dChip

label: Biotin

source_name: Retinal ganglion cell layer

label_protocol: Briefly, 1.5 rounds of cRNA amplification were accomplished using a Ribo-AmpÂ® OA RNA amplification protocol (Arcturus). First strand cDNA was generated by reverse transcription using the total RNA. After the second strand cDNA was synthesized, a T7 RNA polymerase-driven cRNA synthesis was performed to obtain the first round of cRNA amplification. A second double strand cDNA synthesis was performed followed by a second round of cRNA amplification. A BioArrayTM HighYieldTM RNA transcript labeling protocol (T7) (Enzo Life Sciences, Famingdale, NY) was employed for the second round of amplification to biotinylate the cRNAs.

extract_protocol: Frozen sections, mounted on special membrane-coated slides (P.A.L.M. Microbeam) were briefly (1 min) stained with hematoxylin (HistoGeneTM; Arcturus, Mountain View, CA).  Retinal ganglion cells to be isolated were outlined with a light pen to define the area that would be cut and catapulted intact into a Capsure Macro LCM cap (Molecular Devices, Sunnyvale, CA). In this manner, 6000 retinal ganglion cells were isolated from each eye yielding about 60 ng of total cellular RNA.

tag: C57BL/6J, Gender:Male,Age:60-120days


title: LMPC-derived phloem_2

description: RNA amplification was based on the BD-SMART mRNA amplification kit (BD Biosciences Heidelberg, Germany). Prior to in vitro transcription full length cDNAs were pre-amplified with 10 PCR cycles (95° C 30 sec., 60° C 1 min, 68° C 10 min) using the T7 extension of the PCR-Primer II A of the kit.

hyb_protocol: Affymetrix protocol..

source_name: Phloem tissue

label_protocol: Affymetrix protocol..

growth_protocol: Plants were cultivated under short day conditions (8 h light, 22 °C / 16 h darkness, 16 °C) a growth chamber (Percival Scientific, Inc. USA).

tag: Phloem tissue (parenchyma cell, companion cell, sieve element) was excised by LMPC from inflorescence stalk cross sections of Arabidopsis thaliana (ecotype Col-0).


title: Eye with optic nerve crush 3

description: Crush 3


title: Noninjured eye 1


title: Eye with optic nerve crush 1


title: LMPC-derived phloem_3


title: T6 leaf-well watered-rep1

description: T6 leaf-well watered-rep1

source_name: transgenic line (T6) leaf, well watered, replicate 1


title: Noninjured eye 3

description: Control 3


title: ileum_control_2

city: Charleston

first: Stephen

middle: A

last: Duncan

state: SC

address: 173 Ashley Avenue, BSB 6th Floor, Room 657A

department: Regenerative Medicine and Cell Biology

institute: Medical University South Carolina

description: Background and Aims:  Although the zinc finger transcription factor GATA4 has been implicated in regulating jejunal gene expression, the contribution of GATA4 in controlling jejunal physiology has not been addressed. Methods: We generated mice in which the Gata4 gene was specifically deleted in the small intestinal epithelium.  Measurements of plasma cholesterol and phospholipids, intestinal absorption of dietary fat and cholesterol, and gene expression were performed on these animals. Results: Mice lacking GATA4 in the intestine displayed a dramatic block in their ability to absorb cholesterol and dietary fat. Comparison of the global gene expression profiles of control jejunum, control ileum, and GATA4 null jejunum by gene array analysis demonstrated that GATA4 null jejunum lost expression of 53% of the jejunal-specific gene set and gained expression of 47% of the set of genes unique to the ileum. These alterations in gene expression included a decrease in mRNAs encoding lipid and cholesterol transporters as well as an increase in mRNAs encoding proteins involved in bile acid absorption. Conclusion: Our data demonstrate that GATA4 is essential for jejunal function including fat and cholesterol absorption and confirm that GATA4 plays a pivotal role in determining jejunal versus ileal identity.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Standard GCOS data processing produced the values shown.

source_name: ileum, control, 2

label_protocol: Affymetrix One-cycle target labeling

extract_protocol: RNeasy mini kit (Qiagen)

tag: Gata4Loxp/+VillinCre adult male ileum (6-8 wk). Control sample


title: ileum_control_3

source_name: ileum, control, 3

tag: Gata4Loxp/+VillinCre adult male ileum (6-8 wk). Control sample.


title: Phloem exudate_2

description: Microarray analysis were conducted at The Microarray Facility, University of Tuebingen Germany. RNA of the sample was subjected to two rounds of linear amplification using Affymetrix “Two-Cycle cDNA synthesis kit” (Affymetrix, Santa Clara, CA) according to the manufacturer’s instructions.


title: jejunum_GATA4mutant_3

source_name: jejunum, GATA4 mutant, 3

tag: Gata4Loxp/-VillinCre adult male jejunum (6-8wk). Gata4 conditional knockout (mutant) sample.


title: ileum_control_1

source_name: ileum, control, 1


title: pmr5 pmr6 double mutant without treatment, biological rep3

city: Berkeley

first: Shauna

last: Somerville

address: 130 Calvin Hall, Mail Code 5230

department: Energy Biosciences Institute

institute: University of California at Berkeley

description: Gene expression data from 3 weeks old rosette.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner 2500.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS1.2) using Affymetrix default analysis settings with the target intensity set to 500.

source_name: Arabidopsis rosette

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA.

growth_protocol: The plants were grown at 22°C with 14 hrs photoperiod

treatment_protocol: no treatment before collection

tag: Genotype

value: pmr5 pmr6 double mutant

tag: Age

value: 3 weeks old plants


title: jejunum_GATA4mutant_1

source_name: jejunum, GATA4 mutant, 1

tag: Gata4Loxp/-VillinCre adult male jejunum (6-8wk). GATA4 conditional knockout (mutant) sample.


title: pmr5 pmr6 double mutant without treatment, biological rep1


title: Eye with optic nerve crush 2

description: Crush 2


title: pmr6 mutant without treatment, biological rep1

value: pmr6 mutant


title: jejunum_GATA4mutant_2

source_name: jejunum, GATA4 mutant, 2


title: jejunum_control_1

source_name: jejunum, control, 1

tag: Gata4loxP/+VillinCre adult male jejunum (6-8 wk). Control sample.


title: jejunum_control_3

source_name: jejunum, control, 3

tag: Gata4LoxP/+VillinCre adult male jejunum (6-8 wk). Control sample.


title: pmr5 pmr6 double mutant without treatment, biological rep2


title: LMPC-derived phloem_1

description: RNA amplification was based on the BD-SMART mRNA amplification kit (BD Biosciences, Heidelberg, Germany). Prior to in vitro transcription full length cDNAs were pre-amplified with 10 PCR cycles (95° C 30 sec., 60° C 1 min, 68° C 10 min) using the T7 extension- and the PCR-Primer II A of the kit.


title: pmr6 mutant without treatment, biological rep3


title: jejunum_control_2

source_name: jejunum, control, 2


title: pmr6 mutant without treatment, biological rep2


title: pmr5 mutant without treatment, biological rep3

value: pmr5 mutant


title: Mouse immune cells time zero control (mcw018)

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: See manuscript

data_processing: MAS 5.0 as implemented in GCOS

label: Standard Affymetrix label

source_name: mouse immune cells time zero (control)

label_protocol: Standard Affymetrix protocol

extract_protocol: See manuscript

tag: BL6 NOD2-/-


title: Col-0 without treatment, biological rep3


title: pmr5 mutant without treatment, biological rep1


title: Mouse immune cells time 4 hrs after ttreatment (mcw046)

description: See manuscript

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing: MAS 5.0 implemented in GCOS

source_name: mouse immune cells time 4 hrs after ttreatment

label_protocol: Standard Affymetrix Protocol

extract_protocol: See Manuscript

tag: BL6 Wild type


title: Mouse immune cells time 1hr after treatment (mcw033)

description: See manuscript

source_name: mouse immune cells time 1hr after treatment


title: pmr5 mutant without treatment, biological rep2


title: Mouse immune cells time 1hr after treatment (mcw014)

description: See manuscript


title: Mouse immune cells time zero control (mcw012)

description: See manuscript


title: Mouse immune cells time 4 hrs after treatment (mcw016)

description: See manuscript

source_name: mouse immune cells at time 4 hrs after treatment


title: Mouse immune cells time zero control  (mcw044)

description: See manuscript


title: Mouse immune cells time 1 hr after treatment (mcw020)

description: See manuscript

source_name: mouse immune cells 1 hr after treatment

tag: BL6 NOD2 -/-


title: Mouse immune cells time zero control (mcw035)

description: See manuscript


title: Mouse immune cells time 4 hrs after treatment (mcw037)

description: See manuscript

source_name: mouse immune cells time 4 hrs after treatment


title: Mouse immune cells time 4 hrs after treatment (mcw022)

description: See manuscript


title: Mouse immune cells time 4 hrs after treatment (mcw034)

description: See manuscript


title: Mouse immune cells time zero control (mcw032)

description: See manuscript

source_name: mouse immune cells at time zero (control)


title: Mouse immune cells time 1hr after treatment (mcw036)

description: See manuscript

source_name: mouse immune cells time 1hr


title: Col-0 without treatment, biological rep1


title: sid2 mutant with H2O treatment, biological rep1

description: Gene expression data from 4 weeks old rosette.

growth_protocol: The plants were grown in the Percival chamber at 22°C with 14 hr photoperiod

treatment_protocol: H2O or 300 uM BTH spray 2 days before collection

value: sid2 mutant

value: 4 weeks old plants


title: sid2 mutant with H2O treatment, biological rep4


title: Mouse immune cells time 4 hr after treatment (mcw049)

description: See manuscript

source_name: mouse immune cells time 4 hr


title: Col-0 without treatment, biological rep2


title: Donor3, hCMV seropositive healthy donor

city: Salamanca

first: Arancha

last: Rodríguez-Caballero

address: Avda. Universidad de Coimbra. Campus Unamuno

country: Spain

institute: Cancer Research Center. University of Salamanca.

description: hCMV-stimulated (specific) CD69+ CD4+ T-lymphocytes isolated from human peripheral blood of male hCMV-seropositive healthy donor

hyb_protocol: Following fragmentation, 25 microg of cRNA were hybridized to the HG-U133 Plus 2.0 Array chip (Affymetrix) according to the protocols provided by the manufacturer.

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

data_processing: RNA expression values for each probe set were calculated using the RMA (“Robust Multi-array Average”) algorithm.

label_protocol: 100 ng of total RNA from the purified cell fractions was amplified and labeled using the GeneChip two cycle cDNA synthesis kit and the GeneChip IVT labeling kit (Affymetrix Inc., Santa Clara, CA), respectively.

extract_protocol: RNA was extracted using the silica membrane technology NucleoSpinRNA XS (Macherey-Nagel, Düren, Germany)

tag: Donor identifier

tag: Sex

tag: Cell purity of  98%


title: sid2 mutant with H2O treatment, biological rep2


title: Mouse immune cells time zero control (mcw047)

description: See manuscript


title: Donor4, hCMV seropositive healthy donor

tag: hCMV-stimulated (specific) CD69+ CD4+ T-lymphocytes isolated from human peripheral blood of male hCMV-seropositive healthy donor


title: Donor5, hCMV seropositive healthy donor

source_name: hCMV-stimulated (specific) CD69+ CD4+ T-lymphocytes isolated from human peripheral blood


title: mil4 sid2 double mutant with H2O treatment, biological rep3

value: mil4 sid2 double mutant


title: Donor2, hCMV seropositive healthy donor


title: mil4 sid2 double mutant with H2O treatment, biological rep4


title: Mouse immune cells 1 hr after treatment (mcw051)

description: See manuscript

source_name: mouse immune cells 1 hr


title: mil4 with BTH treatment, biological rep4

source_name: Arabidopsis rosette


title: Donor1, hCMV seropositive healthy donor

value: Jose Mo


title: mil4 sid2 double mutant with H2O treatment, biological rep2


title: mil4 with BTH treatment, biological rep2


title: mil4 sid2 double mutant with H2O treatment, biological rep1


title: mil4 with BTH treatment, biological rep1


title: Mouse immune cells 1 hr after treatment (mcw054)

description: See manuscript


title: Case 4F, patient with TCRVbeta13.1+/CD4+/Nka+/CD8-/+ dim T-LGL lymphocytosis

description: Freshly isolated monoclonal CD4+ T-LGL from peripheral blood of female patient with TCRVbeta13.1+/CD4+ T-LGL lymphocytosis

source_name: Freshly isolated monoclonal CD4+ T-LGL from human peripheral blood

extract_protocol: Total RNA was isolated from magnetic-activated cell sorter (MACS)-freshly purified unstimulated monoclonal CD4+ T-LGL lymphocytes from PB sample (purity of ≥98%). To get pure and highly concentrated RNA, the silica membrane technology NucleoSpin® RNA XS (Macherey-Nagel, Düren, Germany) was used.

tag: Patient identifier

value: Female

tag: Cell purity of ≥ 98%


title: Case 2Sp, patient with TCRVbeta13.1+/CD4+/Nka+/CD8-/+ dim T-LGL lymphocytosis

description: purified CD69+ hCMV-stimulated monoclonal CD4+ T-LGL from peripheral blood of female patient with TCRVbeta13.1+/CD4+ T-LGL lymphocytosis

source_name: purified CD69+ hCMV-stimulated monoclonal CD4+ T-LGL from human peripheral blood


title: mil4 with H2O treatment, biological rep4


title: Case 4Sp, patient with TCRVbeta13.1+/CD4+/Nka+/CD8-/+ dim T-LGL lymphocytosis

tag: purified CD69+ hCMV-stimulated monoclonal CD4+ T-LGL from peripheral blood of female patient with TCRVbeta13.1+/CD4+ T-LGL lymphocytosis


title: mil4 with H2O treatment, biological rep2


title: Col with BTH treatment, biological rep3


title: Case 2F, patient with TCRVbeta13.1+/CD4+/Nka+/CD8-/+ dim T-LGL lymphocytosis

tag: Freshly isolated monoclonal CD4+ T-LGL from peripheral blood of female patient with TCRVbeta13.1+/CD4+ T-LGL lymphocytosis


title: mil4 with H2O treatment, biological rep3


title: Case 3Sn, patient with TCRVbeta11+/CD4+/Nka+/CD8-/+ dim T-LGL lymphocytosis

description: purified CD69- hCMV-stimulated monoclonal CD4+ T-LGL from peripheral blood of male patient with TCRVbeta11+/CD4+ T-LGL lymphocytosis

source_name: purified CD69- hCMV-stimulated monoclonal CD4+ T-LGL from human peripheral blood


title: Col with BTH treatment, biological rep4


title: Case 2Sn, patient with TCRVbeta13.1+/CD4+/Nka+/CD8-/+ dim T-LGL lymphocytosis

description: purified CD69- hCMV-stimulated monoclonal CD4+ T-LGL from peripheral blood of female patient with TCRVbeta13.1+/CD4+ T-LGL lymphocytosis


title: Case 4Sn, patient with TCRVbeta13.1+/CD4+/Nka+/CD8-/+ dim T-LGL lymphocytosis

tag: purified CD69- hCMV-stimulated monoclonal CD4+ T-LGL from peripheral blood of female patient with TCRVbeta13.1+/CD4+ T-LGL lymphocytosis


title: Case 3F, patient with TCRVbeta11+/CD4+/Nka+/CD8-/+ dim T-LGL lymphocytosis

description: Freshly isolated monoclonal CD4+ T-LGL from peripheral blood of male patient with TCRVbeta11+/CD4+ T-LGL lymphocytosis


title: Col with BTH treatment, biological rep2

tag: Genotype


title: Case 1Sn, patient with TCRVbeta13.1+/CD4+/Nka+/CD8-/+ dim T-LGL lymphocytosis

description: purified CD69- hCMV-stimulated monoclonal CD4+ T-LGL from peripheral blood of male patient with TCRVbeta13.1+/CD4+ T-LGL lymphocytosis


title: Col with BTH treatment, biological rep1

tag: Age


title: mil4 with H2O treatment, biological rep1


title: Col with H2O treatment, biological rep4


title: Case 1Sp, patient with TCRVbeta13.1+/CD4+/Nka+/CD8-/+ dim T-LGL lymphocytosis

description: purified CD69+ hCMV-stimulated monoclonal CD4+ T-LGL from peripheral blood of male patient with TCRVbeta13.1+/CD4+ T-LGL lymphocytosis


title: Col with H2O treatment, biological rep3


title: Col with H2O treatment, biological rep1


title: 24 hr 10H5, replicate 2

city: south San Francisco

first: Jerry

last: Tang

address: 1 DNA Way MS 93

institute: Genentech Inc

description: Gene expression data from SK-N-AS treated with 10H5 for 24 hours, replicate 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 19 hr at 45C with 60 rpm rotation on Human genome U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymterix GeneChip scanner 3000.

data_processing: Data analysis was performed using the Affymetrix GeneChip operating system and analysis software. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: human SK-N-AS neuroblastoma xenografts, treated with 10H5 for 24 hr

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

growth_protocol: SK-N-AS cells were grown in RPMI, with 10%FBS and 2mM L-Glutamine. 10 million SK-N-AS cells were inoculated into each nude mouse on the right flank subcutaneusly.

extract_protocol: Tumors were collected at indicated time points flash frozen. RNA extraction procedure were perfomed follow manufacturer's recommendation (QIAGEN, Rneasy mini kit cat#74104)

treatment_protocol: Each mouse was dosed with either vehicle (PBS) or 10H5 (5 mg/kg) i.p.

tag: Human neuroblastoma cell line SK-N-AS was implanated into nude mice and treated with anti-IGF1R antibody 10H5 for 24 hours


title: mil4 overexpression line with BTH treatment, biological rep2

value: mil4 overexpression line


title: vehicle, biological replicate 3

description: Gene expression data from vehicle treated SK-N-AS, replicate 3

source_name: human SK-N-AS neuroblastoma xenografts, vehicle

tag: Human neuroblastoma cell line SK-N-AS was implanated into nude mice and treated with vehicle control GP120


title: mil4 overexpression line with BTH treatment, biological rep4


title: 24 hr 10H5, replicate 3

description: Gene expression data from SK-N-AS treated with 10H5 for 24 hours, replicate 3


title: vehicle, biological replicate 4

description: Gene expression data from vehicle treated SK-N-AS, replicate 4


title: 24 hr 10H5, replicate 1

description: Gene expression data from SK-N-AS treated with 10H5 for 24 hours, replicate 1


title: 24 hr 10H5, replicate 4

description: Gene expression data from SK-N-AS treated with 10H5 for 24 hours, replicate 4


title: vehicle, biological replicate 1

description: Gene expression data from vehicle treated SK-N-AS, replicate 1


title: mil4 overexpression line with BTH treatment, biological rep3


title: vehicle, biological replicate 2

description: Gene expression data from vehicle treated SK-N-AS, replicate 2


title: mil4 overexpression line with BTH treatment, biological rep1

description: Gene expression data from 4 weeks old rosette.


title: mil4 overexpression line with H2O treatment, biological rep4


title: mil4 overexpression line with H2O treatment, biological rep2


title: mil4 with BTH treatment, biological rep3


title: mil4 overexpression line with H2O treatment, biological rep1


title: BMPR2 mutation carrier 180 with no clinical disease

city: Nashville

first: James

last: West

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

description: EBV-immortalized B cells from 66 year old male with BMPR2 mutation but no sign of pulmonary arterial hypertension.

hyb_protocol: following Affymetrix GeneChip Expression Analysis Manual

data_processing: Affymetrix chp and cel files

source_name: EBV-immortalized B-cells

extract_protocol: RNA was extracted from freshly cultured lymphoblastoid cells using a Qiagen RNeasy kit.


title: sid2 mutant with H2O treatment, biological rep3


title: BMPR2 mutation carrier 186 with clinical PAH

description: EBV-immortalized B cells from 29 year old male with BMPR2 mutation and clinical pulmonary arterial hypertension

scan_protocol: following Affymetrix GeneChip Expression Analysis Manual


title: Col with H2O treatment, biological rep2


title: BMPR2 mutation carrier 723 with clinical PAH

description: EBV-immortalized B cells from 35 year old female with BMPR2 mutation and clinical pulmonary arterial hypertension

label_protocol: following Affymetrix GeneChip Expression Analysis Manual


title: mil4 overexpression line with H2O treatment, biological rep3


title: BMPR2 mutation carrier 172 with no clinical disease

description: EBV-immortalized B cells from 65 year old female with BMPR2 mutation but no sign of pulmonary arterial hypertension.


title: BMPR2 mutation carrier 264 with clinical PAH

description: EBV-immortalized B cells from 17 year old female with BMPR2 mutation and clinical pulmonary arterial hypertension


title: S58-2_2 with array type ATH1 from Affymetrix

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: In order to identify new genes implicated in ABA signalisation pathways, we have carried out a screen for suppressor mutants of the ABA deficient mutant aba3-1. Infrared thermography was used to identify plants whose cold leaf phenotype was reverted. The transcriptome analysis of four recessive suppressor mutants was undertaken to determine which genes are differentially expressed compared to the wild type or aba3-1. Such genes could represent the mutated gene itself or indicate signalling or response pathways affected by the mutation

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label_protocol: labelling Biotin direct, amplification=yes, RNAa 20 ug.

growth_protocol: aerial - compost/ 70 per cent/ 21degreeC/ 8h00 light 16h00 dark

treatment_protocol: no treatment

tag: Arabidopsis thaliana (col-0)  mutant (supS58-2) - harvest date:29-09-06


title: S58-2_1 with array type ATH1 from Affymetrix

tag: Arabidopsis thaliana (col-0)  mutant (supS58-2) - harvest date:10-07-06


title: wt_2 with array type ATH1 from Affymetrix

growth_protocol: aerial - compost/ 70per cent/ 21degreeC/ 8h00 light 16h00 dark

tag: Arabidopsis thaliana (col-0)  - harvest date:29-09-06


title: BMPR2 mutation carrier 266 with clinical PAH

description: EBV-immortalized B cells from 39 year old male with BMPR2 mutation and clinical pulmonary arterial hypertension


title: aba3-1_2 with array type ATH1 from Affymetrix

tag: Arabidopsis thaliana (col-0)  mutant (aba3-1) - harvest date:29-09-06


title: S15-118_2 with array type ATH1 from Affymetrix

tag: Arabidopsis thaliana (col-0)  mutant (supS15-118) - harvest date:29-09-06


title: S14-150_2 with array type ATH1 from Affymetrix

tag: Arabidopsis thaliana (col-0)  mutant (supS14-150) - harvest date:29-09-06


title: BMPR2 mutation carrier 176 with no clinical disease

description: EBV-immortalized B cells from 88 year old female with BMPR2 mutation but no sign of pulmonary arterial hypertension.


title: S82-2_2 with array type ATH1 from Affymetrix

tag: Arabidopsis thaliana (col-0)  mutant (supS82-2) - harvest date:29-09-06


title: Primary peripheral blood B cell (resting) -repeat1 - mAdbID:68995

description: mAdb experiment ID: 68995

hyb_protocol: Affymetrix Hybridization Protocol Other: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on LymphDX Custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing:
MAS 5.0 Data Processing Protocol
Calculation Method: The data were analyzed with Microarray Suite version 5.0 (MA S 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: B cell - resting

extract_protocol:
Trizol Total RNA
Extraction method: Trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

tag: Cell type

value: Primary peripheral blood B cell


title: Primary peripheral blood B cell (resting) -repeat2 - mAdbID:68978

description: mAdb experiment ID: 68978


title: Primary peripheral blood B cell antiIgM -1hr - mAdbID:68979

description: mAdb experiment ID: 68979

source_name: B cell antiIgM - 1 hour

treatment_protocol:
Treatment type: compound
Agent: anti_IgM
Treatment dose: 25ug/ml
Treatment time: 1 hour
Treatment temperature: 37C
In-vivo treatment: CD19+ peripheral blood B cells Rx w/ anti_IgM


title: Primary peripheral blood B cell antiIgM -3hr - mAdbID:68980

description: mAdb experiment ID: 68980

source_name: B cell antiIgM - 3 hour

treatment_protocol:
Treatment type: compound
Agent: anti_IgM
Treatment dose: 25ug/ml
Treatment time: 3 hour
Treatment temperature: 37C
In-vivo treatment: CD19+ peripheral blood B cells Rx w/ anti_IgM


title: S15-118_1 with array type ATH1 from Affymetrix

tag: Arabidopsis thaliana (col-0)  mutant (supS15-118) - harvest date:10-07-06


title: JJN3 - mAdbID:79766

description: mAdb experiment ID: 79766

extract_protocol:
Trizol Total RNA
Extraction method: trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

value: Myeloma


title: S14-150_1 with array type ATH1 from Affymetrix

tag: Arabidopsis thaliana (col-0)  mutant (supS14-150) - harvest date:10-07-06


title: LP1 - mAdbID:79769

description: mAdb experiment ID: 79769


title: Jeko - mAdbID:76650

description: mAdb experiment ID: 76650

source_name: Jeko

value: MCL


title: aba3-1_1 with array type ATH1 from Affymetrix

tag: Arabidopsis thaliana (col-0)  mutant (aba3-1) - harvest date:10-07-06


title: Case 3Sp, patient with TCRVbeta11+/CD4+/Nka+/CD8-/+ dim T-LGL lymphocytosis

description: purified CD69+ hCMV-stimulated monoclonal CD4+ T-LGL from peripheral blood of male patient with TCRVbeta11+/CD4+ T-LGL lymphocytosis

tag: Patient identifier

tag: Sex

tag: Cell purity of ≥ 98%


title: wt_1 with array type ATH1 from Affymetrix

tag: Arabidopsis thaliana (col-0)  - harvest date:10-07-06


title: BJAB - mAdbID:69818

description: mAdb experiment ID: 69818

source_name: BJAB

value: GCB-DLBCL


title: DB - mAdbID:69800

description: mAdb experiment ID: 69800

source_name: DB


title: S82-2_1 with array type ATH1 from Affymetrix

tag: Arabidopsis thaliana (col-0)  mutant (supS82-2) - harvest date:10-07-06


title: KMS11 - mAdbID:68991

description: mAdb experiment ID: 68991


title: JIM3 - mAdbID:68994

description: mAdb experiment ID: 68994


title: KMS12 - mAdbID:68992

description: mAdb experiment ID: 68992


title: H1112 - mAdbID:68990

description: mAdb experiment ID: 68990


title: WT adult murine BM, LSK FLT3- (LIN-SCA1+KIT+FLT3-) #1

status: Public on Aug 31 2008

city: Lund

first: Robert

last: Månsson

address: Klinikgatan 26, BMC B12

department: Hemapotoietic stem cell biology

country: Sweden

institute: Lund University

description: Gene expression data from WT LMPP cells FACS sorted from adult BM

hyb_protocol: Following fragmentation, 10 microg of cRNA was hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned using an Affymetrix GeneChip Scanner 3000. Chip target intensity was arbitrarily scaled to 100 before rendering CHP files.

data_processing: Expression values were calculated by RMA express (http://rmaexpress.bmbolstad.com/) using background adjustment and quantile normalization.

source_name: Murine BM from C57bl/6 mice

label_protocol: Biotinylated cRNA was prepared according to the standard AffymetrixTM; Small Sample Labelling Protocol v.2, with the exception that the second round of in vitro transcription (IVT) was performed using AffymetrixTM GeneChipTM Expression 3’amplification kit.

extract_protocol: Cells were directly sorted into buffer RLT and RNA prepared using RNeasy Micro (Qiagen) according to manufacturer's instructions.

tag: Wild type C57bl/6


title: LB84-1 - mAdbID:68988

description: mAdb experiment ID: 68988

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).


title: WT adult murine BM, LMPP (LIN-SCA1+KIT+FLT3hi) #1


title: Mino - mAdbID:76647

description: mAdb experiment ID: 76647

source_name: Mino


title: WT adult murine BM, LMPP (LIN-SCA1+KIT+FLT3hi) #2


title: OciLy19 - mAdbID:66127

description: mAdb experiment ID: 66127


title: Z138 - mAdbID:76648

description: mAdb experiment ID: 76648


title: UPN1 - mAdbID:76649

description: mAdb experiment ID: 76649


title: E2A-KO adult murine BM, LMPP (LIN-SCA1+KIT+FLT3hi) #2

source_name: Murine BM from E2A-KO mice on C57bl/6 background.

tag: E2A-KO C57bl/6


title: OciLy7 - mAdbID:66126

description: mAdb experiment ID: 66126


title: WT adult murine BM, LSK FLT3- (LIN-SCA1+KIT+FLT3-) #2


title: control, biological replicate 2

city: Beijing

first: Jinye

last: Mu

address: Datun Road, Chaoyang District,Beijing,China

country: China

institute: Institute of Genetics and Developmental Biology,CAS

description: RNA prepared from 4-day-old pER8-LEC1 transgenic seedlings germinated and grown in the absence (control) of 0.01mM of estradiol.

hyb_protocol: Standard Affymetrix protocols. Samples were submitted to Expression Analysis Inc. (Gene Tech,CN) for hybridization to Affymetrix ATH1 microarrays.

data_processing: MAS 5

source_name: 0.1% DMSO

label_protocol: Fragmented cRNA probes were prepared using the two-cycle amplification protocol by Affymetrix.

growth_protocol: Seeds were surface sterilized with 10% Bleach for 5 minutes and then rinsed 3 times with sterile water.Standard media is 0.5X concentration Murashige and Skoog salt mixture (Sigma),  3% sucrose, 0.8% agar and adjusted to pH 5.7 with KOH. The plate was kept at 4oC for 2-3 days and then transferred to a tissue culture room germinated and grown at 22oC under continuous white light.

extract_protocol: Approximately 100 mg plants were collected per replicate. Samples were briefly sonicated to disrupt the tissue. RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH).

treatment_protocol: Transgenic plants seeds were sowed on 1/2 MS medium plus 0.1% DMSO. Seedlings were grown for 4 days. Whole seedlings were collected into RNA extraction buffer. Approximately 100 mg were collected per replicate, with two biological replicates being performed.

tag: Ecotype

value: Columbia

tag: Age

value: Whole seedlings taken 4 days after germination

tag: Growth Media

value: Standard media plus 0.1% DMSO

tag: Treatment length

value: 4 days


title: eye, retina: Diabetes 3_le1

status: Public on Aug 30 2008

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description: Total retinal RNA extracted from six total retinas from three mice who have had experimentally induced diabetes for 3-4 weeks.

source_name: eye, retina

tag: tissue

value: retina

tag: disease state

value: Diabetes


title: eye, retina: Diabetic 1_le1

description: Total retinal RNA extracted from four total retinas from two mice who have had streptozotocin-induced diabetes for 5 weeks.


title: estradiol induced, biological replicate 2

description: RNA prepared from 4-day-old pER8-LEC1 transgenic seedlings germinated and grown in the presence of 0.01mM of estradiol.

scan_protocol: Standard Affymetrix protocols. Samples were submitted to Expression Analysis Inc. (Gene Tech,CN) for hybridization to Affymetrix ATH1 microarrays.

source_name: 0.01mM estradiol

treatment_protocol: Transgenic plants seeds were sowed on 1/2 MS medium plus chemical inducer (estradiol). Seedlings were grown for 4 days. Whole seedlings were collected into RNA extraction buffer. Approximately 100 mg were collected per replicate, with two biological replicates being performed.

value: Standard media plus 0.01mM estradiol


title: control, biological replicate 1

description: RNA prepared from 4-day-old pER8-LEC1 transgenic seedlings germinated and grown in the absence (control) of 0.01mM estradiol.


title: brain, lateral and medial ganglionic eminences: Arx-/Y #2_le1

description: Total RNA (Trizol + RNeasy cleanup) extracted from E14.5 ganglionic eminence (left and right, medial and lateral) from Arx-/Y Brn4Cre+ SRY+ mouse.


title: estradiol induced, biological replicate 1


title: brain, lateral and medial ganglionic eminences: Arx+/Y #1_le1

description: Total RNA (Trizol + RNeasy cleanup) extracted from E14.5 ganglionic eminence (left and right, medial and lateral) from Arx+/Y Brn4Cre+ SRY+ (wild-type control) mouse.


title: brain, lateral and medial ganglionic eminences: Arx-/Y#1_le1


title: brain, lateral and medial ganglionic eminences: Arx+/Y #4_le1


title: eye, retina: Control 1_le1

description: Total retinal RNA extracted from four retinas from two mice who are age-matched with the diabetic mice but have not undergone treatment and have normal blood-glucose levels.

value: Control


title: brain, lateral and medial ganglionic eminences: Arx+/Y #2_le1


title: eye, retina: Diabetes 2_le1

description: Total retinal RNA extracted from four retinas from two mice who have had streptozotocin-induced diabetes for 5 weeks.


title: brain, lateral and medial ganglionic eminences: Arx+/Y #3_le1


title: E2A-KO adult murine BM, LMPP (LIN-SCA1+KIT+FLT3hi) #1


title: eye, retina: Control 2_le1


title: brain, lateral and medial ganglionic eminences: Arx-/Y #4_le1


title: brain, lateral and medial ganglionic eminences: Arx-/Y #3_le1


title: Frontonasal E12.5 biological replicate 4

city: Aurora

first: Trevor

last: Williams

state: CO

department: Craniofacial Biology

institute: UCHSC at Fitzsimons

description: Frontonasal prominence tissue from mouse embryos at E12.5 days, pooled from 3-4 embryos

hyb_protocol: Biotinylated cRNA probes in 200 ul sample buffer were hybridized to Affymetrix GeneChip Mouse 430 2.0 microarrays which contain probes corresponding to 39,000 mouse transcripts at 45C for 16 hr in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA.).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA.).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol: Total RNA (2-5 ug) was converted to double-stranded cDNA (ds-cDNA) using the Superscript Choice System (Life Technologies, Inc.) and oligo-dT primer containing a T7 RNA polymerase promoter (Genset Corp.). After the second strand synthesis the reaction mixture was extracted with phenol chloroform-isoamyl alcohol and the ds-cDNA was recovered by ethanol precipitation. In vitro transcription was performed to generate biotin-labeled cRNA using an RNA Transcript Labeling Kit (Enzo. Inc.) and 3.3 uL ds-cDNA template in the presence of a mixture of biotin-labeled ribonucleotides. Biotin-labeled cRNA was then purified using an RNeasy affinity column (Qiagen). Next, the cRNA was fragmented to ensure optimal hybridization to the oligonucleotide array. Fragmentation was performed such that the cRNA fragments are between 35-200 bp in length by incubating the cRNA at 94C for 35 min in a fragmentation buffer. The sample was then added to a hybridization solution containing 100 mM MES, 1 M NaCl, and 20 mM EDTA in the presence of 0.01% Tween 20. The final concentration of the fragmented cRNA was 0.05 ug/uL. Labeled cRNA probes were generated from total RNA samples using the GeneChip Expression 3' Amplification One-Cycle Target Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Following mating and visualization of a vaginal plug, pregnant females were sacrificed between E10 and E12.5 depending on the time-point under study. Mice employed for the E10, E11, and E12 timepoints were housed in a reverse light cycle room to facilitate dissections at midday for all samples.

extract_protocol: Tissue pools were dissolved in 1ml Trizol (Invitrogen) and total RNA was extracted according to the manufacturer's instructions and resuspended in a final volume of 100ul DEPC treated water. Subsequently, the sample was further purified using the RNeasy Mini Kit protocol (Qiagen, Inc.). The concentration of each total RNA sample was determined based on the absorbance at 260 nm (A260). The quality of each sample was first determined based on the ratio of A260 to A280 and samples in the range of 1.9-2.1 were considered adequately pure to be employed in cDNA synthesis. The integrity and purity of the individual samples from each prominence were also assessed using RT-PCR. Total RNA (1-2ug) was used for cDNA synthesis using random primers and Superscript III reverse transcriptase (Invitrogen) according to the manufacturer's instructions. Subsequently, 2ul of the cDNA mixture was used for PCR in a 25ul reaction with Accuprime Taq DNA polymerase (Invitrogen) using the following conditions: 1 cycle at 94C for 3 min; 35 cycles at 94C for 45 sec, 58C for 45 sec, 68C for 1 min; and 1 cycle at 68C for 10 min. Specific primers were directed against transcripts that were diagnostic of the facial prominences including Tcfap2a, Dlx-2, Bmp2, and Gsc, or would detect contamination from adjacent tissue, e.g. Zic3 for forebrain tissue. Significantly contaminated or degraded RNA samples were discarded.

treatment_protocol: Embryos were dissected from the uterus in ice-cold DEPC-PBS medium and then individually placed into drops of DEPC-PBS media in a petri dish. Embryos were then staged by plug time and craniofacial features. After staging, each embryo was bisected with forceps at the level of the heart and the caudal portion was discarded. Tungsten needles were employed to isolate the combined maxillary and mandibular prominences and these were then separated into their individual components. Next, the medial and lateral frontonasal prominences were removed from the remainder of the head. Briefly, an incision was made in the ectoderm overlying the prominences to produce a flap of ectoderm that was peeled back with the loosely aggregated cells of the mesenchyme still attached. Note that if the cut was made too deep and extends into the forebrain region, loosely packed mesenchymal cells were no longer visible. These latter samples that were potentially contaminated with forebrain tissue were discarded. Suitably pure maxillary, mandibular, and frontonasal samples were placed in separate tubes containing RNAlater (Ambion) and stored at -20C for later pooling and processing. Pooling was necessary to obtain sufficient RNA for screening of the microarrays.

tag: Strain

value: embryonic day 12.5

tag: Tissue

value: Frontonasal prominence


title: Frontonasal E12.5 biological replicate 6

source_name: Frontonasal prominence tissue from mouse embryos at E12.5 days


title: Frontonasal E12.5 biological replicate 2


title: Frontonasal E12.5 biological replicate 1


title: Frontonasal E11.0 biological replicate 5

description: Frontonasal prominence tissue from mouse embryos at E11.0 days, pooled from 8-9 embryos

value: embryonic day 11.0


title: Frontonasal E11.0 biological replicate 3

source_name: Frontonasal prominence tissue from mouse embryos at E11.0 days


title: Frontonasal E11.0 biological replicate 7


title: Frontonasal E12.5 biological replicate 7


title: Frontonasal E11.5 biological replicate 1

description: Frontonasal prominence tissue from mouse embryos at E11.5 days, pooled from 8-9 embryos

value: embryonic day 11.5


title: Frontonasal E11.0 biological replicate 4


title: Frontonasal E11.5 biological replicate 3

source_name: Frontonasal prominence tissue from mouse embryos at E11.5 days


title: Frontonasal E12.0 biological replicate 6

description: Frontonasal prominence tissue from mouse embryos at E12.0 days, pooled from 3-4 embryos

value: embryonic day 12.0


title: Frontonasal E11.5 biological replicate 4


title: Frontonasal E11.5 biological replicate 6


title: Frontonasal E11.0 biological replicate 2


title: Frontonasal E11.5 biological replicate 2


title: Frontonasal E11.0 biological replicate 6


title: Frontonasal E12.5 biological replicate 5


title: Frontonasal E12.0 biological replicate 7

source_name: Frontonasal prominence tissue from mouse embryos at E12.0 days


title: Frontonasal E12.0 biological replicate 2


title: Frontonasal E12.0 biological replicate 1


title: Frontonasal E12.0 biological replicate 5


title: Frontonasal E12.0 biological replicate 3


title: Frontonasal E11.0 biological replicate 1


title: Frontonasal E11.5 biological replicate 7


title: Frontonasal E10.5 biological replicate 7

description: Frontonasal prominence tissue from mouse embryos at E10.5 days, pooled from 24-28 embryos

value: embryonic day 10.5


title: Frontonasal E11.5 biological replicate 5


title: Frontonasal E12.5 biological replicate 3


title: Frontonasal E10.5 biological replicate 3

source_name: Frontonasal prominence tissue from mouse embryos at E10.5 days


title: Frontonasal E12.0 biological replicate 4


title: Frontonasal E10.5 biological replicate 6


title: Frontonasal E10.5 biological replicate 5


title: Frontonasal E10.5 biological replicate 4


title: Maxillary E12.5 biological replicate 7

description: Maxillary prominence tissue from mouse embryos at E12.5 days, pooled from 3-4 embryos

value: Maxillary prominence


title: Frontonasal E10.5 biological replicate 1


title: Frontonasal E10.5 biological replicate 2


title: Maxillary E12.5 biological replicate 6

source_name: Maxillary prominence tissue from mouse embryos at E12.5 days


title: Maxillary E12.0 biological replicate 3

description: Maxillary prominence tissue from mouse embryos at E12.0 days, pooled from 3-4 embryos


title: Maxillary E12.5 biological replicate 4


title: Maxillary E11.5 biological replicate 2

description: Maxillary prominence tissue from mouse embryos at E11.5 days, pooled from 8-9 embryos


title: Maxillary E12.0 biological replicate 7

source_name: Maxillary prominence tissue from mouse embryos at E12.0 days


title: Maxillary E11.0 biological replicate 4

description: Maxillary prominence tissue from mouse embryos at E11.0 days, pooled from 8-9 embryos


title: Maxillary E11.0 biological replicate 7

source_name: Maxillary prominence tissue from mouse embryos at E11.0 days


title: Maxillary E12.0 biological replicate 2


title: Maxillary E11.5 biological replicate 6

source_name: Maxillary prominence tissue from mouse embryos at E11.5 days


title: Maxillary E11.5 biological replicate 3


title: Maxillary E11.5 biological replicate 4


title: Maxillary E11.0 biological replicate 1


title: Maxillary E12.5 biological replicate 3


title: Maxillary E12.0 biological replicate 4


title: Maxillary E11.5 biological replicate 1


title: Maxillary E12.0 biological replicate 5


title: Maxillary E12.0 biological replicate 6


title: Maxillary E11.0 biological replicate 2


title: Maxillary E11.5 biological replicate 7


title: Maxillary E11.0 biological replicate 5


title: Maxillary E12.5 biological replicate 2


title: Maxillary E12.5 biological replicate 5


title: Maxillary E11.0 biological replicate 6


title: Maxillary E11.5 biological replicate 5


title: Maxillary E12.5 biological replicate 1


title: Maxillary E12.0 biological replicate 1


title: Maxillary E11.0 biological replicate 3


title: Maxillary E10.5 biological replicate 7

description: Maxillary prominence tissue from mouse embryos at E10.5 days, pooled from 24-28 embryos


title: Maxillary E10.5 biological replicate 6

source_name: Maxillary prominence tissue from mouse embryos at E10.5 days


title: Maxillary E10.5 biological replicate 2


title: Mandibular E12.0 biological replicate 7

description: Mandibular prominence tissue from mouse embryos at E12.0 days, pooled from 3-4 embryos

value: Mandibular prominence


title: Mandibular E12.5 biological replicate 4

description: Mandibular prominence tissue from mouse embryos at E12.5 days, pooled from 3-4 embryos


title: Mandibular E12.5 biological replicate 7

source_name: Mandibular prominence tissue from mouse embryos at E12.5 days


title: Maxillary E10.5 biological replicate 4


title: Mandibular E12.5 biological replicate 6


title: Mandibular E12.5 biological replicate 5


title: Mandibular E12.5 biological replicate 2


title: Mandibular E11.5 biological replicate 6

description: Mandibular prominence tissue from mouse embryos at E11.5 days, pooled from 8-9 embryos


title: Mandibular E12.0 biological replicate 5

source_name: Mandibular prominence tissue from mouse embryos at E12.0 days


title: Mandibular E12.5 biological replicate 1


title: Mandibular E11.5 biological replicate 5

source_name: Mandibular prominence tissue from mouse embryos at E11.5 days


title: Maxillary E10.5 biological replicate 5


title: Mandibular E12.0 biological replicate 3


title: Mandibular E12.0 biological replicate 4


title: Mandibular E11.5 biological replicate 7


title: Mandibular E12.5 biological replicate 3


title: Maxillary E10.5 biological replicate 1


title: Maxillary E10.5 biological replicate 3


title: Mandibular E11.0 biological replicate 6

description: Mandibular prominence tissue from mouse embryos at E11.0 days, pooled from 8-9 embryos


title: Mandibular E12.0 biological replicate 2


title: Mandibular E11.5 biological replicate 3


title: Mandibular E12.0 biological replicate 6


title: Mandibular E11.5 biological replicate 2


title: Mandibular E11.0 biological replicate 7

source_name: Mandibular prominence tissue from mouse embryos at E11.0 days


title: Mandibular E11.5 biological replicate 4


title: Mandibular E12.0 biological replicate 1


title: Mandibular E11.5 biological replicate 1


title: K562 cells CREB Knock-out replicate 10

city: los angeles

first: matteo

last: pellegrini

address: 610 charles young drive east

institute: UCLA

hyb_protocol: RNA samples were labeled and hybridized by standard protocol to Affymetrix GeneChip Human Genome  U133+ Array Set HG-U133A array

source_name: K562 cells CREB Knock-out

tag: K562 (Iscoves + 10% FCS) and TF-1 (RPMI + 10%FCS + rhGM-CSF.  Cells were cultured at 37oC, 5% CO2 and split every 3 to 4 days.  The CREB specific shRNA sequences were selected and validated based on accepted parameters established by Tuschl et al.


title: Mandibular E11.0 biological replicate 4


title: Mandibular E10.5 biological replicate 7

description: Mandibular prominence tissue from mouse embryos at E10.5 days, pooled from 24-28 embryos


title: K562 cells control replicate 4

hyb_protocol: RNA samples were labeled and hybridized by standard protocol to Affymetrix GeneChip Human Genome  U133+ Array Set HG-U133A array.

source_name: K562 cells

tag: K562 (Iscoves + 10% FCS) and TF-1 (RPMI + 10%FCS + rhGM-CSF.  Cells were cultured at 37oC, 5% CO2 and split every 3 to 4 days.


title: Mandibular E11.0 biological replicate 5


title: Mandibular E11.0 biological replicate 2


title: Mandibular E10.5 biological replicate 5

source_name: Mandibular prominence tissue from mouse embryos at E10.5 days


title: Mandibular E10.5 biological replicate 2


title: Mandibular E10.5 biological replicate 1


title: K562 cells CREB Knock-out replicate 8

scan_protocol: RNA samples were labeled and hybridized by standard protocol to Affymetrix GeneChip Human Genome  U133+ Array Set HG-U133A array


title: K562 cells control replicate 9

label_protocol: RNA samples were labeled and hybridized by standard protocol to Affymetrix GeneChip Human Genome  U133+ Array Set HG-U133A array

tag: K562 (Iscoves + 10% FCS) and TF-1 (RPMI + 10%FCS + rhGM-CSF.  Cells were cultured at 37oC, 5% CO2 and split every 3 to 4 days


title: K562 cells CREB Knock-out replicate 9

extract_protocol: RNA samples were labeled and hybridized by standard protocol to Affymetrix GeneChip Human Genome  U133+ Array Set HG-U133A array


title: Mandibular E11.0 biological replicate 3


title: Mandibular E10.5 biological replicate 4


title: Mandibular E11.0 biological replicate 1


title: Mandibular E10.0 biological replicate 7

description: Mandibular prominence tissue from mouse embryos at E10.0 days, pooled from 40-48 embryos

value: embryonic day 10.0


title: K562 cells CREB Knock-out replicate 7

tag: K562 (Iscoves + 10% FCS) and TF-1 (RPMI + 10%FCS + rhGM-CSF.  Cells were cultured at 37oC, 5% CO2 and split every 3 to 4 days. The CREB specific shRNA sequences were selected and validated based on accepted parameters established by Tuschl et al.


title: Mandibular E10.5 biological replicate 6


title: K562 cells CREB Knock-out replicate 6

tag: K562 (Iscoves + 10% FCS) and TF-1 (RPMI + 10%FCS + rhGM-CSF.  Cells were cultured at 37oC, 5% CO2 and split every 3 to 4 days.  . The CREB specific shRNA sequences were selected and validated based on accepted parameters established by Tuschl et al.


title: K562 cells CREB Knock-out replicate 2

tag: K562 (Iscoves + 10% FCS) and TF-1 (RPMI + 10%FCS + rhGM-CSF.  Cells were cultured at 37oC, 5% CO2 and split every 3 to 4 days. . The CREB specific shRNA sequences were selected and validated based on accepted parameters established by Tuschl et al.


title: K562 cells control replicate 7


title: K562 cells CREB Knock-out replicate 4


title: K562 cells CREB Knock-out replicate 1


title: K562 cells CREB Knock-out replicate 5


title: K562 cells control replicate 5


title: K562 cells CREB Knock-out replicate 3


title: K562 cells control replicate 6


title: K562 cells control replicate 8


title: Mandibular E10.5 biological replicate 3


title: Arabidopsis vip3_2

city: East Lansing

first: Sookyung

last: Oh

state: MI

department: Horticulture

institute: Michigan State University

description: Each of two replicates for each genotypes was composed of three independently derived samples. Each sample included more than 100 plants.

hyb_protocol: Affymetrix GeneChip Expression Analysis Technical Manual

data_processing: Microarray data were analyzed using the statistical algorithms within the Affymetrix Microarray Suite (MAS) 5.0 software.

source_name: Arabidopsis 14 day old seedling for vip3

extract_protocol: Total RNA was isolated using Qiagen RNAeasy columns (Qiagen, Valencia, CA)


title: K562 cells control replicate 3


title: Mandibular E10.0 biological replicate 4

source_name: Mandibular prominence tissue from mouse embryos at E10.0 days


title: Mandibular E10.0 biological replicate 2


title: Arabidopsis WT-1 seedling

scan_protocol: Affymetrix GeneChip Expression Analysis Technical Manual

source_name: Arabidopsis 14 day old seedling

tag: Arabidopsis wild-type


title: Mandibular E10.0 biological replicate 5


title: Arabidopsis vip3_1

label_protocol: Affymetrix GeneChip Expression Analysis Technical Manual

tag: Arabidopsis 14 day old seedling for vip3


title: Mandibular E10.0 biological replicate 3


title: Mandibular E10.0 biological replicate 1


title: Gfi1 ko

status: Public on Aug 26 2008

city: Braunschweig

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: Gfi1 ko

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: Gfi1-/- splenic B cells

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

growth_protocol: ex vivo

extract_protocol: RNeasy

value: B-cells from spleen

tag: B220+CD19+ CD138- B cells of 4 week old mice


title: Arabidopsis WT-2

source_name: Arabidopsis Wild-type 14 day old seedling

tag: Arabidopsis wild-type 14 day old seedling


title: Mandibular E10.0 biological replicate 6

tag: Age


title: K562 cells control replicate 1

scan_protocol: RNA samples were labeled and hybridized by standard protocol to Affymetrix GeneChip Human Genome  U133+ Array Set HG-U133A array.

data_processing: MAS 5.0


title: K562 cells control replicate 2

label_protocol: RNA samples were labeled and hybridized by standard protocol to Affymetrix GeneChip Human Genome  U133+ Array Set HG-U133A array.


status: Public on Aug 23 2008

city: Singapore

first: Jaichandran

last: Sivalingam

address: 11 Hospital Drive

department: Division of Medical Sciences

country: Singapore

institute: National Cancer Center

description: Transcriptome dataset of human umbilical cord lining epithelial cells.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized to the Affymetrix HG-U133A chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Genecip scanner 3000 7G.

data_processing: The data were condensed with MAS 5.0 using the Affymetrix software using default settings. The normalization target was set to 500.

label_protocol: Biotinylated cRNA were prepared from 8 microg total RNA using the IVT labelling kit (Affymetrix).

growth_protocol: Establised primary cultures were cultured in pTTE1 (provided by CellResearch Corporation) medium.

extract_protocol: Total RNA was extracted using Triazol reagent according to manufacturer's protocol.

treatment_protocol: No Treatment

tag: Human Umbilical Cord lining Epithelial cells ID #33

tag: Gender

value: Female

tag: Karyotype

value: 46 XX, Normal

tag: In vitro Passage Number


title: GFP integrated Human Umbilical Cord lining Epithelial cells

description: Transcriptome dataset of human umbilical cord lining epithelial cells with EGFP integration.

treatment_protocol: EGFP cDNA integrated into genomic DNA using phage integrase.

tag: Integrated with EGFP cDNA using Phage Integrase


title: Gfi1 wt

description: Gfi1 wt

source_name: Gfi1+/+ splenic B cells

tag: tissue


title: K562 cells control replicate 10


title: single cell from posterior mesoderm (E/MB), biological rep10

status: Public on Aug 22 2008

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

country: Japan

institute: Nara Medical University

description: Gene expression data from posterior mesoderm cell (E/MB)

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic Target Hybridization)

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix)

data_processing: CEL data were generated by GeneChip Operating Software and then subjected to the dCHIP software.  Data were normalized together with the default settings.  The Model-Based Expression Indices (MBEI) were calculated using the PM/MM difference mode with log-2 transformation of signal intensity and truncation of low values to zero.  The absolute calls were calculated using MAS5.0 algorism with dCHIP default settings.

source_name: single cell from posterior mesoderm cells at base of allantois at E/MB (Blimp1-, Oct4+, Hoxb1+)

label_protocol: Biotinylated cRNA were prepared from the PCR-amplified double-starnded cDNA according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual, 2004, Affymetrix: Eukaryotic One-Cycle Target Labeling Assay)

growth_protocol: Mice were sacrified and embryos were collected in Dulbecco’s modified Eagle Medium supplemented with 0.5% BSA (DMEM/BSA) at different days post coitum (dpc).  Noon of the day when the vaginal plugs of the mated females were identified was scored as 0.5 dpc.

extract_protocol: Single cell was lysed by adding to the tube containing cell lysis buffer, and the clude lysate was used for cDNA synthesis and amplification without purification.

treatment_protocol: Embryos were dissected in DMEM/BSA.  Embryonic fragments containing primordial germ cells (PGCs) or PGC precursors were cut out by glass needle and incubated with 0.05% trypsin/0.5 mM EDTA for 7 min, followed by dissociation into single cells by mouth pipette.  Dissociated single cells were randomly picked up for single cell cDNA amplification.

tag: Strain

tag: Genotype

value: Wild type

tag: cDNA amplified from single cellular RNA


title: single cell from posterior mesoderm (E/MB), biological rep2


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (E/MB), biological rep9

description: Gene expression data from BlimpKO Blimp1-null-transcrip-positive cell (E/MB)

source_name: single cell from BlimpKO Blimp1-null-transcrip-positive, Oct4+ cells at E/MB


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (E/MB), biological rep12


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (E/MB), biological rep11


title: single cell from posterior mesoderm (E/MB), biological rep8


title: single cell from posterior mesoderm (E/MB), biological rep5


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (E/MB), biological rep6


title: single cell from posterior mesoderm (E/MB), biological rep3


title: single cell from posterior mesoderm (E/MB), biological rep9


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (E/MB), biological rep3


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep20

description: Gene expression data from BlimpKO Blimp1-null-transcrip-positive cell (LS/0B)

source_name: single cell from BlimpKO Blimp1-null-transcrip-positive, Oct4+ cells at LS/0B


title: single cell from posterior mesoderm (E/MB), biological rep6


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (E/MB), biological rep7


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (E/MB), biological rep4


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (E/MB), biological rep10


title: single cell from posterior mesoderm (E/MB), biological rep1


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (E/MB), biological rep8


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep15


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep18


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep17


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (E/MB), biological rep1


title: single cell from posterior mesoderm (E/MB), biological rep4


title: single cell from posterior mesoderm (E/MB), biological rep7


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep13


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep16


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep14


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep19


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (E/MB), biological rep2


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep12


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep9


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (E/MB), biological rep5


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep6


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep7


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep8


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep10


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep1


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep5


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep4


title: single cell from Blimp1+, Hoxb1+ cells (E/MB), biological rep6

description: Gene expression data from Blimp1+, Hoxb1+ cells (EHF)

source_name: single cell from Blimp1+, Oct4, Hoxb1+ cells at EHF stage


title: single cell from Blimp1+, Hoxb1+ cells (E/MB), biological rep7


title: single cell from Blimp1+, Hoxb1+ cells (E/MB), biological rep4

description: Gene expression data from Blimp1+, Hoxb1+ cells (E/MB)

source_name: single cell from Blimp1+, Oct4+, Hoxb1+ cells at E/MB stage


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep3


title: single cell from Blimp1+, Hoxb1+ cells (E/MB), biological rep1


title: single cell from Blimp1+, Hoxb1+ cells (E/MB), biological rep3


title: single cell from Blimp1+, Hoxb1+ cells (E/MB), biological rep8


title: single cell from Blimp1+, Hoxb1+ cells (E/MB), biological rep2


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep2


title: single cell from BlimpKO Blimp1-null-transcrip-positive cells (LS/0B), biological rep11


title: single cell from PGCs (E8.25), biological rep8

description: Gene expression data from single PGCs (E8.25)

source_name: single cell from primordial germ cell (PGCs) at Embryonic day (E) 8.25(Blimp1+, stella+)


title: single cell from PGCs (E8.25), biological rep7


title: single cell from PGCs (E8.25), biological rep2


title: single cell from PGCs (E8.25), biological rep5


title: single cell from Blimp1+, Hoxb1+ cells (E/MB), biological rep5


title: single cell from PGCs (Early-Head Fold stage), biological rep6

description: Gene expression data from single PGCs (Early head fold stage)

source_name: single cell from primordial germ cell (PGCs) at Early head fold stage(Blimp1+, stella+)


title: single cell from PGCs (E8.25), biological rep6


title: single cell from PGCs (E8.25), biological rep1


title: single cell from PGCs (Early-Head Fold stage), biological rep8


title: single cell from PGCs (E8.25), biological rep4


title: single cell from PGCs (E8.25), biological rep3


title: single cell from PGCs (Early-/Mid-bud stage), biological rep4

description: Gene expression data from single PGCs (Early/Mid bud stage)

source_name: single cell from primordial germ cell (PGCs) at Early-/Mid-bud stage (Blimp1+, stella+)


title: single cell from PGCs (Early-/Mid-bud stage), biological rep7


title: single cell from PGCs (Early-Head Fold stage), biological rep4


title: single cell from PGCs (Early-Head Fold stage), biological rep5


title: single cell from PGCs (Early-/Mid-bud stage), biological rep8


title: single cell from PGCs (Early-Head Fold stage), biological rep3


title: single cell from PGCs (Early-/Mid-bud stage), biological rep6


title: single cell from PGCs (Early-/Mid-bud stage), biological rep3


title: single cell from PGCs (Early-Head Fold stage), biological rep1


title: single cell from PGCs (Early-/Mid-bud stage), biological rep1


title: single cell from PGCs (Early-/Mid-bud stage), biological rep5


title: single cell from PGCs (Early-/Mid-bud stage), biological rep2


title: single cell from lineage-restricted PGC precursors (Early/Mid-Streak stage), biological rep7

description: Gene expression data from single lineage-restricted PGC precursors (Early/Mid-Streak stage)

source_name: single cell from lineage-restricted PGC precursors at Early/Mid-Streak stage(Blimp1+, Oct4+)


title: single cell from lineage-restricted PGC precursors (Early/Mid-Streak stage), biological rep6


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep16

description: Gene expression data from single lineage-restricted PGC precursors (Late-Streak/0-Bud stage)

source_name: single cell from lineage-restricted PGC precursors at Late-Streak/0-Bud stage(Blimp1+, Oct4+)


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep21


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep23


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep14


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep20


title: single cell from lineage-restricted PGC precursors (Early/Mid-Streak stage), biological rep1


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep19


title: single cell from lineage-restricted PGC precursors (Early/Mid-Streak stage), biological rep5


title: single cell from lineage-restricted PGC precursors (Early/Mid-Streak stage), biological rep2


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep22


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep18


title: single cell from lineage-restricted PGC precursors (Early/Mid-Streak stage), biological rep4


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep24


title: single cell from lineage-restricted PGC precursors (Early/Mid-Streak stage), biological rep3


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep7


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep6


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep8


title: single cell from lineage-restricted PGC precursors (Late-Streak/0-Bud stage), biological rep1