title: whole-blood_1_pair-78


title: whole-blood_0_pair-76

status: Public on Mar 01 2011

type: RNA

city: CA

first: James

middle: A.

last: Wingrove

state: CA

address: 2500 Faber Place

country: USA

institute: CardioDx, Inc.

hyb_protocol: Labeled RNAs were hybridized using the Agilent protocol

scan_protocol: Agilent Feature Extraction Software (version 10.2.1.3) was used for background subtraction and LOWESS normalization.

data_processing: Agilent processed signal values were used;  values were scaled to a trimmed mean of 100 using an R script developed in-house at CardioDx.

molecule: total RNA

organism: Homo sapiens

label_protocol: 200 ng of each patient whole blood RNA was labeled with Cy3 using Agilent's Low RNA Input Linear Amplification Kit following the recommended protocol.

growth_protocol: Whole blood (2.5 ml) was collected via syringe prior to catheterization.

extract_protocol: RNA was extracted using a magnetic bead-based approach (Agencourt RNAdvance) on an automated platform (Hamilton Star)

treatment_protocol: Collected blood was aliquoted into PaxGene tubes, inverted 10X and then frozen at -20 C until further processing

tag: disease state

value: Control (0)

tag: pair

value: pair 76

tag: sex (gender)

value: Female

tag: date of birth

tag: smoking status

value: Never


title: whole-blood_1_pair-74

value: Case (1)

value: pair 74


title: whole-blood_0_pair-73

value: pair 73

value: Male

value: Quit within last 2 months


title: whole-blood_0_pair-77

value: pair 77


title: whole-blood_1_pair-71

value: pair 71

value: Quit more than 2 months ago


title: whole-blood_1_pair-72

value: pair 72


title: whole-blood_1_pair-75

value: pair 75


title: whole-blood_0_pair-71


title: whole-blood_1_pair-70

value: pair 70


title: whole-blood_0_pair-68

value: pair 68


title: whole-blood_1_pair-68

value: Current


title: whole-blood_1_pair-69

value: pair 69


title: whole-blood_1_pair-7

value: pair 7


title: whole-blood_0_pair-69

value: Control (0)


title: whole-blood_0_pair-72


title: whole-blood_0_pair-70


title: whole-blood_0_pair-67

value: pair 67


title: whole-blood_1_pair-66

value: Case (1)

value: pair 66

value: Never


title: whole-blood_0_pair-66

value: Male


title: whole-blood_1_pair-63

value: pair 63


title: whole-blood_1_pair-67


title: whole-blood_0_pair-63


title: whole-blood_1_pair-60

value: pair 60


title: whole-blood_0_pair-60


title: whole-blood_0_pair-55

value: pair 55


title: whole-blood_0_pair-57

value: pair 57


title: whole-blood_0_pair-59

value: pair 59


title: whole-blood_1_pair-58

value: pair 58

value: Female


title: whole-blood_0_pair-6

value: pair 6

value: Quit more than 2 months ago


title: whole-blood_0_pair-64

value: pair 64

value: Current


title: whole-blood_1_pair-55


title: whole-blood_1_pair-59


title: whole-blood_1_pair-56

value: pair 56


title: whole-blood_0_pair-58

value: Control (0)


title: whole-blood_1_pair-54

value: Case (1)

value: pair 54


title: whole-blood_0_pair-54


title: whole-blood_1_pair-6


title: whole-blood_0_pair-56

value: Never


title: whole-blood_1_pair-57

value: Male


title: whole-blood_1_pair-53

value: pair 53


title: whole-blood_1_pair-51

value: pair 51


title: whole-blood_0_pair-5

value: pair 5


title: whole-blood_1_pair-5


title: whole-blood_0_pair-51


title: whole-blood_1_pair-50

value: pair 50


title: whole-blood_0_pair-53


title: whole-blood_0_pair-50


title: whole-blood_0_pair-48

value: pair 48


title: whole-blood_1_pair-64


title: whole-blood_1_pair-48


title: whole-blood_1_pair-46

value: pair 46


title: whole-blood_1_pair-49

value: pair 49

value: Female


title: whole-blood_0_pair-49


title: whole-blood_0_pair-47

value: pair 47


title: whole-blood_0_pair-46

value: Quit more than 2 months ago


title: whole-blood_1_pair-47


title: whole-blood_1_pair-43

value: pair 43


title: whole-blood_1_pair-44

value: pair 44

value: Quit within last 2 months


title: whole-blood_0_pair-39

value: Control (0)

value: pair 39

value: Current


title: whole-blood_1_pair-40

value: Case (1)

value: pair 40

value: Never


title: whole-blood_0_pair-42

value: pair 42

value: Male


title: whole-blood_1_pair-4

value: pair 4


title: whole-blood_0_pair-44


title: whole-blood_1_pair-41

value: pair 41


title: whole-blood_0_pair-43


title: whole-blood_1_pair-42


title: whole-blood_0_pair-38

value: pair 38


title: whole-blood_0_pair-41


title: whole-blood_0_pair-40

value: Female


title: whole-blood_0_pair-4


title: whole-blood_1_pair-38


title: whole-blood_1_pair-39


title: whole-blood_1_pair-33

value: pair 33


title: whole-blood_1_pair-37

value: pair 37


title: whole-blood_1_pair-34

value: pair 34


title: whole-blood_0_pair-36

value: pair 36

value: Quit more than 2 months ago


title: whole-blood_0_pair-31

value: Control (0)

value: pair 31


title: whole-blood_0_pair-34

value: Quit within last 2 months


title: whole-blood_1_pair-35

value: Case (1)

value: pair 35


title: whole-blood_1_pair-36

value: Current


title: whole-blood_0_pair-35

value: Never


title: whole-blood_0_pair-33

value: Male


title: whole-blood_0_pair-32

value: pair 32


title: whole-blood_0_pair-37


title: whole-blood_1_pair-32


title: whole-blood_0_pair-7

value: pair 7


title: whole-blood_0_pair-30

value: pair 30


title: whole-blood_1_pair-31


title: whole-blood_1_pair-30


title: whole-blood_1_pair-3

value: pair 3


title: whole-blood_1_pair-28

value: pair 28

value: Female


title: whole-blood_0_pair-27

value: pair 27


title: whole-blood_1_pair-27


title: whole-blood_0_pair-25

value: pair 25


title: whole-blood_0_pair-28

value: ND


title: whole-blood_1_pair-25


title: whole-blood_1_pair-23

value: pair 23

value: Quit more than 2 months ago


title: whole-blood_1_pair-29

value: pair 29


title: whole-blood_1_pair-22

value: Case (1)

value: pair 22


title: whole-blood_0_pair-23

value: Control (0)


title: whole-blood_0_pair-26

value: pair 26

value: Never


title: whole-blood_1_pair-24

value: pair 24


title: whole-blood_0_pair-21

value: pair 21


title: whole-blood_0_pair-2

value: pair 2

value: Male


title: whole-blood_0_pair-22


title: whole-blood_1_pair-20

value: pair 20


title: whole-blood_1_pair-17

value: pair 17


title: whole-blood_0_pair-24

value: Female


title: whole-blood_1_pair-21


title: whole-blood_0_pair-29


title: whole-blood_1_pair-26


title: whole-blood_1_pair-2

value: Current


title: whole-blood_0_pair-17


title: whole-blood_0_pair-20


title: whole-blood_1_pair-15

value: pair 15


title: whole-blood_1_pair-16

value: pair 16


title: whole-blood_1_pair-13

value: pair 13


title: whole-blood_0_pair-16

value: Quit more than 2 months ago


title: whole-blood_0_pair-15


title: whole-blood_0_pair-13


title: whole-blood_1_pair-12

value: Case (1)

value: pair 12


title: whole-blood_1_pair-113

value: pair 113


title: whole-blood_0_pair-113

value: Control (0)


title: whole-blood_0_pair-115

value: pair 115

value: Never


title: whole-blood_0_pair-12


title: whole-blood_1_pair-115


title: whole-blood_0_pair-112

value: pair 112


title: whole-blood_1_pair-11

value: pair 11


title: whole-blood_1_pair-111

value: pair 111

value: Male


title: whole-blood_1_pair-106

value: pair 106


title: whole-blood_1_pair-107

value: pair 107

value: Female


title: whole-blood_0_pair-111


title: whole-blood_0_pair-108

value: pair 108

value: Current


title: whole-blood_0_pair-106


title: whole-blood_0_pair-11


title: whole-blood_0_pair-109

value: pair 109


title: whole-blood_0_pair-107


title: whole-blood_1_pair-110

value: pair 110


title: whole-blood_1_pair-112

value: Case (1)


title: whole-blood_0_pair-110

value: Quit more than 2 months ago


title: whole-blood_1_pair-109


title: whole-blood_0_pair-105

value: pair 105


title: whole-blood_1_pair-108


title: whole-blood_1_pair-105


title: whole-blood_0_pair-104

value: Control (0)

value: pair 104


title: whole-blood_0_pair-3

value: pair 3


title: whole-blood_0_pair-10

value: pair 10


title: whole-blood_1_pair-10


title: whole-blood_1_pair-102

value: pair 102

value: Never


title: whole-blood_1_pair-104

value: Male


title: whole-blood_0_pair-102


title: whole-blood_0_pair-100

value: pair 100


title: whole-blood_1_pair-1

value: pair 1


title: whole-blood_0_pair-1


title: whole-blood_1_pair-100

value: Female


title: whole-blood_0_pair-103

value: pair 103


title: whole-blood_1_pair-103

value: Quit within last 2 months


title: spleen follicular B in WT, biological rep2

status: Public on Dec 20 2010

city: Seoul

first: Dong-Mi

last: Shin

address: 1 gwanak-ro

country: South Korea

institute: seoul national university

description:
Gene expression data spleen follicular B in WT
A combination of CD23, CD21 and CD19 markers was included in the sorting scheme. PE-labeled anti-CD23 Ab was used to give a satisfying separation of MZ and FO B cells. MZ B cells were sorted as B220+CD21BriCD23-. FO B cells were sorted as B220+CD21loCD23+

hyb_protocol: Five micrograms of labeled target from twenty-four submitted samples (received 2-10-09) was combined with 2X hybridization buffer, 3nM B2 control oligo (Affymetrix 900457), 20X spike in (Affymetrix 51214), and DMSO making a final volume of 100ul for the twenty-four individual hybridizations to the commercial Affymetrix GeneChip, mouse gene 1.0 ST containing the Mus musculus genome.  The hybridization cocktail, including the components listed above, was denatured for five minutes at 99◦C then transferred to a 45◦C heat block for an additional five minutes before transferring 80ul of the cocktail into the chip.  The hybridization was carried out at a constant temperature of 45◦C for approximately seventeen hours using the Affymetrix 640 oven 500k approved.

scan_protocol: Upon completion of the fluidics process, each sample was scanned using the Affymetrix GeneChip 3000 7Gplus scanner to create the image files (dat).  GeneChip Operating Software (GCOS v1.4) was then used to convert the image files to cel files

data_processing: Data were collected using GeneChip Operating Software (GCOS v1.4). The robust multiarray average (RMA) and quantile normalization were performed.

label: biotin

organism: Mus musculus

label_protocol: Total of 5 µg of double stranded cDNA was concentrated to 25 µL.  Each sample was combined with 5 µL fragmentation buffer mix (FL1) and 2 µL fragmentation enzyme mix (FL2).  DNA was digested at 37 °C for 30 minutes and enzyme was denatured at 95 °C for 2 minutes.  Fragmented ds cDNAs were biotin end-labeled using terminal transferase.  Each fragmented sample was combined with15 μl labeling buffer mix (FL3), 1.5 μl biotinylated nucleotides (FL4), 1.5 μl terminal transferase (FL5), incubated at 37 °C for 60 minutes, and heat inactivated.

extract_protocol: Antibody stained spleen cells were sorted using FACS Aria Cell-Sorting System (Beckton-Dickinson, Franklin Lake, NJ) and either 104 Marginal zone (MZ) cells or 104 follicular (FO) B cells were directly collected into RLT buffer (Qiagen, Valencia, CA). lysates were thawed in room temperature and genomic DNA was fragmented to by spinning the samples through Qiashredder columns for 2 minutes at 21,000 x g.  To RLT buffer sample was added to 100% ethanol and RNAs were extracted using Qiagen RNeasy 96-well system as described previously (Virtaneva et al., 2005).  As contaminating gDNA will interfere with the downstream Nugen Ribo-SPIA™ technology, each RNA sample were treated with 27 units of DNAse I (Qiagen, Valencia, CA) for 15 minutes at room temperature during extraction.  RNA yield was estimated using Nanodrop (NanoDrop Technologies, Wilmington, DE) and 2100 Bioanalyzer (Agilent Technologies, Santa Clare, CA).

tag: cells

value: spleen follicular B cells

tag: genotype

value: WT

tag: genetic background


title: spleen follicular B in WT, biological rep5

source_name: Gene expression data spleen follicular B in WT


title: spleen follicular B in IRF8 conditional KO, biological rep1

description:
Gene expression data spleen follicular B in IRF8 conditional KO
A combination of CD23, CD21 and CD19 markers was included in the sorting scheme. PE-labeled anti-CD23 Ab was used to give a satisfying separation of MZ and FO B cells. MZ B cells were sorted as B220+CD21BriCD23-. FO B cells were sorted as B220+CD21loCD23+

value: IRF8 KO

value: C57BL/6J-lrf8-/- x CD19-Cre


title: spleen follicular B in IRF8 conditional KO, biological rep6

source_name: Gene expression data spleen follicular B in IRF8 conditional KO


title: spleen follicular B in WT, biological rep6


title: spleen marginal zone B in IRF8 conditional KO, biological rep6

description:
Gene expression data spleen marginal zone B in IRF8 conditional KO
A combination of CD23, CD21 and CD19 markers was included in the sorting scheme. PE-labeled anti-CD23 Ab was used to give a satisfying separation of MZ and FO B cells. MZ B cells were sorted as B220+CD21BriCD23-. FO B cells were sorted as B220+CD21loCD23+

value: spleen marginal zone B cells


title: spleen follicular B in IRF8 conditional KO, biological rep5


title: spleen follicular B in IRF8 conditional KO, biological rep4


title: spleen follicular B in IRF8 conditional KO, biological rep3


title: spleen follicular B in WT, biological rep4


title: spleen follicular B in WT, biological rep1


title: spleen follicular B in WT, biological rep3


title: spleen marginal zone B in IRF8 conditional KO, biological rep5

source_name: Gene expression data spleen marginal zone B in IRF8 conditional KO


title: spleen marginal zone B in IRF8 conditional KO, biological rep4


title: spleen marginal zone B in WT, biological rep6

description:
Gene expression data spleen marginal zone B in WT
A combination of CD23, CD21 and CD19 markers was included in the sorting scheme. PE-labeled anti-CD23 Ab was used to give a satisfying separation of MZ and FO B cells. MZ B cells were sorted as B220+CD21BriCD23-. FO B cells were sorted as B220+CD21loCD23+


title: spleen marginal zone B in WT, biological rep5

source_name: Gene expression data spleen marginal zone B in WT


title: spleen marginal zone B in IRF8 conditional KO, biological rep1


title: spleen marginal zone B in WT, biological rep4


title: spleen marginal zone B in IRF8 conditional KO, biological rep2


title: spleen marginal zone B in IRF8 conditional KO, biological rep3


title: Sorted round spermatids, biological rep3

status: Public on Dec 16 2010

city: Jupiter

first: Philippe

middle: R

last: Bois

state: FL

address: 130 Scripps Way

department: Cancer Biology

institute: The Scripps Research Institute - Scripps Florida

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Round Spermatids, rep3.

hyb_protocol: Fragmentation/hybridization to MOE430v2.0 arrays (Affymetrix) were performed according to Affymetrix protocols.

scan_protocol: Imaging was performed on a Hewlett Packard GenEarray Scanner according to standard Affymetrix protocol.

data_processing: The data were analyzed using GeneSpring version 7.3 based on GCRMA analysis default settings.

source_name: Round Spermatids (Testis)

label_protocol: Biotin-labeled cRNA probes were prepared as recommended by the manufacturer (Affymetrix), using oligo-dT primers, SuperScript, and BioArray High Yield RNA Transcript kits (Affymetrix).

extract_protocol: For purified meiotic fractions, RNA was prepared using RNAqueous Micro kits (Ambion) according to recommended protocols.

tag: strain

value: C57BL/6 x DBA/2J

tag: generation

tag: gender

value: male

tag: age

value: 10-16 weeks

tag: tissue

value: testis

tag: meiotic fraction

value: round spermatids

tag: stain

value: Hoechst 33342


title: Sorted round spermatids, biological rep2

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Round Spermatids, rep2.


title: Sorted round spermatids, biological rep4

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Round Spermatids, rep4.


title: spleen marginal zone B in WT, biological rep2


title: spleen marginal zone B in WT, biological rep1


title: Sorted Leptotene/Zygotene, biological rep3

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Leptotene/Zygotene, rep3.

source_name: Leptotene/Zygotene (Testis)

value: leptotene/zygotene


title: Sorted round spermatids, biological rep1

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Round Spermatids, rep1.


title: Sorted mid-Pachytene, biological rep2

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Mid-Pachytene, rep2.

source_name: mid-Pachytene (Testis)

value: mid-pachytene


title: Sorted Diplotene, biological rep1

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Diplotene, rep1.

source_name: Diplotene (Testis)

value: diplotene


title: Sorted Diplotene, biological rep2

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Diplotene, rep2.


title: Sorted mid-Pachytene, biological rep1

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Mid-Pachytene, rep1.


title: Sorted Early-Pachytene

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Early-Pachytene.

source_name: Early-Pachytene (Testis)

value: early-pachytene


title: Sorted pre-Leptotene, biological rep3

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Pre-Leptotene, rep3.

source_name: pre-Leptotene (Testis)

value: pre-leptotene


title: Sorted late-Pachytene

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
late-Pachytene.

source_name: late-Pachytene (Testis)

value: late-pachytene


title: Sorted pre-Leptotene, biological rep2

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Pre-Leptotene, rep2.


title: Sorted Leptotene/Zygotene, biological rep1

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Leptotene/Zygotene, rep1.


title: Sorted Leptotene/Zygotene, biological rep2

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Leptotene/Zygotene, rep2.


title: spleen marginal zone B in WT, biological rep3


title: Sorted pre-Leptotene, biological rep1

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Pre-Leptotene, rep1.


title: Sorted spermatogonia, biological rep2

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Spermatogonia, rep2.

source_name: Spermatogonia (Testis)

value: spermatogonia


title: Sorted spermatogonia, biological rep4

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Spermatogonia, rep4.


title: IL6 and Myc PCT 11

status: Public on Feb 01 2010

hyb_protocol: Chips were prehybridized in a sealed chamber immersed in a 42°C waterbath using established procedures.Chips were then washed twice for 2 min with agitation, first in ultra-pure water, then in isopropyl alcohol. After the last isopropyl alcohol wash, samples were quickly placed in a room-temperature centrifuge and spun dry (3000 rmp, 5 min). The chips were hybridized overnight in a sealed humidified slide chamber immersed in a light-protected 42°C waterbath, then washed, dried, and stored in the dark until scanned.

scan_protocol: Chips were scanned using an Axon 4000B scanner and GenePix 4.0 software. Photomultiplier tube voltage settings were adjusted to allow 1% saturation of signal in both channels.

data_processing: Image data were extracted, and extracted data were normalized with lowess smoothing function. Value is the ratio of Cy3 to Cy5 in log2.

source_name: IL6 and Myc PCT 11

label_protocol:
1. Add primer to the RNA samples to be labeled.
• Make up fresh or thaw previously made Master Mixes B. (See Master Mix Table)
Prime the two RNA samples to be compared
RNA sample (30 μg total RNA per rxn) in dH2O
15 μl
Oligo dT primer (1mg/ml)
1 μl
Total
16 μl
(See notes 1,2,6)
2. Heat and snap cool.
• Heat samples to 70°C for 5 min., then snap cool in an ice-water bath. Centrifuge briefly to collect the contents to the bottom of the tube.
3. Initiate two labeling reactions, one for Cy3 and one for Cy5.
Add these components in the order listed
RNase inhibitor diluted 2X
0.5 μl
Master Mix B
10.0 μl
dUTP-Cy3 OR dUTP Cy5
2.0 μl
Superscript II
1.5 μl
Total Volume should now be 30ul
(See Note 3)
• Mix the components well with the RNA/primer sample and centrifuge briefly to collect the contents to the bottom of the tube
4. Incubate reverse transcription reaction mixture at 42°C for 90 min
5. Degrade RNA
• After the reverse transcription reaction is complete, add 10μl of 1M NaOH and heat at 70oC for 15 min.
• Neutralize with 10μl 1M HCl.
6. Clean up labeled cDNA
• Combine the appropriate Cy3- and Cy5-labeled samples that will be co-hybridized onto the array.
• Add the combined probes to a Vivaspin 500 (10K cutoff) with 400 μl TE. Centrifuge at 12,000 X g (~10,000 rpm) for 8 min. Discard flow through.
• Repeat the wash step in the same Vivaspin filter at least three times.
• We recommend 2-3 additional washes in a fresh Vivaspin 500. Add 400 μl TE, centrifuge at 12,000 X g (~10,000 rpm) for 8 min. Discard flow through.
• Remove the sample retained in the filter chamber with a pipette and transfer to a new tube. Adjust the sample volume to 20 μl for the mouse and human standard microarray formats

extract_protocol:
Extraction protocol 1. Isolate RNA using Trizol Reagent.
• Suspend pelleted cell sample in 1ml of Trizol reagent for each 5-10 x106 cells. Pipette up and down. Some cell types are more difficult to lyse (e.g. yeast or mycobacterium) and may require mechanical disruption in the presence of Trizol reagent. Incubate 5 min.
• Add 0.2x volume (of Trizol used) of Chloroform. Shake tube well. Incubate 2 min.
• Centrifuge at 13,000 x g for 15 min at 4oC and collect upper clear layer.
• This is equivalent to taking the trizol protocol through the phase separation step and then transferring the aqueous phase into the Qiagen RNA clean-up procedure below.
2. Perform Qiagen RNA Clean up procedure
• Perform at room temperature. Add an equal volume of 70% Ethanol to the Trizol upper layer. Mix well and apply to RNeasy spin column. Check product information for capacity of columns.
• Centrifuge Discard flow through. Wash column 2x with RPE buffers supplied in the kit. Be certain ethanol has been added to RPE concentrate before use.
• After the last spin the column is dry so that the Ethanol is removed. Transfer the column to a fresh collection tube.
• Elute RNA with the designated volume of RNase free water. Allow to stand for 1 min then centrifuge collecting the eluted RNA. Repeat one time.

value: spleen PCT

source_name: Reference RNAs

tag: sample type

value: Reference RNA produced from mixed B cell lymphoma cell lines


title: IL6 and Myc PCT 10

source_name: IL6 and Myc PCT 10


title: Boris KO2

status: Public on Mar 31 2010

source_name: Boris KO2

tag: mouse type

value: Boris KO

source_name: normal

extract_protocol:
1. Isolate RNA using Trizol Reagent.
• Suspend pelleted cell sample in 1ml of Trizol reagent for each 5-10 x106 cells. Pipette up and down. Some cell types are more difficult to lyse (e.g. yeast or mycobacterium) and may require mechanical disruption in the presence of Trizol reagent. Incubate 5 min.
• Add 0.2x volume (of Trizol used) of Chloroform. Shake tube well. Incubate 2 min.
• Centrifuge at 13,000 x g for 15 min at 4oC and collect upper clear layer.
• This is equivalent to taking the trizol protocol through the phase separation step and then transferring the aqueous phase into the Qiagen RNA clean-up procedure below.
2. Perform Qiagen RNA Clean up procedure
• Perform at room temperature. Add an equal volume of 70% Ethanol to the Trizol upper layer. Mix well and apply to RNeasy spin column. Check product information for capacity of columns.
• Centrifuge Discard flow through. Wash column 2x with RPE buffers supplied in the kit. Be certain ethanol has been added to RPE concentrate before use.
• After the last spin the column is dry so that the Ethanol is removed. Transfer the column to a fresh collection tube.
• Elute RNA with the designated volume of RNase free water. Allow to stand for 1 min then centrifuge collecting the eluted RNA. Repeat one time.

value: wild type


title: Sorted spermatogonia, biological rep3

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Spermatogonia, rep3.

value: C57BL/6 x DBA/2J


title: Boris KO3

source_name: Boris KO3


title: Boris KO1

source_name: Boris KO1


title: Boris KO5

source_name: Boris KO5


title: Sorted spermatogonia, biological rep1

description:
Gene expression data from FACS-sorted meiotic cells from C57BL/6 x DBA/2J F1 male mice 10-16 weeks old.
Spermatogonia, rep1.

value: male


title: IL6 and Myc PCT 8

source_name: IL6 and Myc PCT 8


title: IL6 and Myc PCT 9

source_name: IL6 and Myc PCT 9


title: IL6 and Myc PCT 1

source_name: IL6 and Myc PCT 1


title: IL6 and Myc PCT 5

source_name: IL6 and Myc PCT 5


title: IL6 and Myc PCT 4

source_name: IL6 and Myc PCT 4


title: IL6 PCT 3

source_name: IL6 PCT 3

value: spleen


title: IL6 and Myc PCT 3

source_name: IL6 and Myc PCT 3


title: IL6 PCT 9

source_name: IL6 PCT9


title: IL6 and Myc PCT 7

source_name: IL6 and Myc PCT 7


title: IL6 and Myc PCT 2

source_name: IL6 and Myc PCT 2


title: IL6 PCT 5

source_name: IL6 PCT 5

source_name: Reference RNAs


title: IL6 PCT 10

source_name: IL6 PCT 10


title: IL6 PCT 7

source_name: IL6 PCT7


title: IL6 PCT 6

source_name: IL6 PCT6


title: IL6 PCT 4

source_name: IL6 PCT4


title: IL6 and Myc PCT 6

source_name: IL6 and Myc PCT 6


title: Boris KO4

source_name: Boris KO4

value: testis

source_name: normal


title: IL6 PCT 1

source_name: IL6 PCT1


title: IL6 PCT 8

source_name: IL6 PCT 8


title: IL6 PCT 2

source_name: IL6 PCT 2


title: spleen follicular B in IRF8 conditional KO, biological rep2

description:
Gene expression data spleen follicular B in IRF8 conditional KO
A combination of CD23, CD21 and CD19 markers was included in the sorting scheme. PE-labeled anti-CD23 Ab was used to give a satisfying separation of MZ and FO B cells. MZ B cells were sorted as B220+CD21BriCD23-. FO B cells were sorted as B220+CD21loCD23+

value: spleen follicular B cells

value: IRF8 KO

value: C57BL/6J-lrf8-/- x CD19-Cre


title: normal5

status: Public on Sep 30 2008

tag: normal spleen from young BALB/cPt

source_name: Reference RNA

label_protocol: same as channel1

extract_protocol: same as channel1

tag: Reference RNA produced from mixed B cell lymphoma cell lines


title: PCT18

tag: mouse PCT 18 from BALB/c-IL6 transgenic mice


title: PCT20

tag: mouse PCT 20 from BALB/c-IL6 transgenic mice


title: PCT15

tag: mouse PCT 15 from BALB/c-IL6 transgenic mice


title: PCT17

tag: mouse PCT 17 from BALB/c-IL6 transgenic mice


title: Normal2


title: Normal1


title: Optic nerves from P35 (adult) wild type

status: Public on Jul 01 2009

city: Bethesda

first: Philip

last: Lee

state: MD

address: 35 Lincoln Drive

institute: NIH/NICHD

description: Investigation of leukemia inhibitory factor effect on oligodendrocyte development and myelination in the postnatal optic nerve

hyb_protocol: 750 ng of biotin-labeled cRNA was hybridized for 16 hours to Illumina Sentrix mouseref-8 expression beadchips

scan_protocol: Hybridized biotinylated cRNA was detected with streptavidin-Cy3 and quantitated using Illuminas beadstation 500GX genetic analysis systems scanner

data_processing: Preliminary analysis of the scanned data was performed using Illumina BeadStudio software.  The primary Illumina data is returned from the scanner in the form of an “.idat” file which contains single intensity data values/gene following the computation of a trimmed mean average for each probe type represented by a variable number of bead probes/gene on the array.  The Bead Studio software returns information on the number and standard deviation of all the bead measurements per probe/gene as well as a detection threshold based on a comparison between the measured intensity calculated for a single probe/gene and the intensities measured for a large number of negative control beads built-in to the BeadChip arrays (D = % above negative/100, 1 = perfect, i.e. the intensity value of a gene is greater than all the intensities for every negative control tested).  Any gene consistently below D=.99 for all samples was eliminated from further analysis. This background filter resulted in the removal of approximately 20% of all the genes on the Illumina array (4,938 background genes out of a total of 24,527 RefSeq genes).  Further filtering removed 1,688 genes without a meaningful HUGO gene name.  Overall differences in gene expression between samples were calculated by a global normalization method based on total intensity counts for each array.  A normalization factor was determined by dividing the average total intensity by the true total intensity. Each intensity value was multiplied by its appropriate normalization factor.

source_name: Optic nerves dissected from P35 (adult) wild type

label_protocol: 500 ng total RNA labelled using the Illumina TotalPrep RNA amplification kit.  Single stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP.

growth_protocol: Optic nerves from LIF knockout and wild type mice. Postnatal day 10- 10 optic nerves, postnatal day 14- 8 optic nerves, postnatal day 35 (adult)- 4 optic nerves

extract_protocol: Total RNA extracted using TRIzol extraction method

treatment_protocol: Optic nerves were not treated after dissection from postnatal mice

tag: genotype

value: CD1 wild type

tag: Sex

tag: cell type

value: 4 optic nerves used


title: PCT16

tag: mouse PCT 16 from BALB/c-IL6 transgenic mice


title: Normal3


title: PCT19

tag: mouse PCT 19 from BALB/c-IL6 transgenic mice


title: Optic nerves from P14 LIF knockout

source_name: Optic nerves dissected from P14 LIF knockout

value: LIF-/- on CD1 background

value: 8 optic nerves used


title: Optic nerves from P10 wild type

source_name: Optic nerves dissected from P10 wild type

value: 10 optic nerves used


title: noraml4


title: Optic nerves from P14 wild type

source_name: Optic nerves dissected from P14 wild type


title: Optic nerves from P10 LIF knockout

source_name: Optic nerves dissected from P10 LIF knockout

growth_protocol: Optic nerves from LIF knockout and wild type mice. Postnatal day 10- 10 optic nerves, postnatal day 14- 8 optic nerves, postnatal day 35 (adult)- 4 optic nerves.

value: optic nerve, 10 used


title: Optic nerves from P35 (adult) LIF knockout

source_name: Optic nerves dissected from P35 (adult) LIF knockout