title: CRH_21

description: Heart tissue from mice that were fed an ad lib diet.

source_name: Mus musculus heart tissue

extract_protocol: RNA was extracted from heart tissue using 1.0mm glass beads (BioSpec Products, Inc.) in a Precellys 24 Tissue Homogenizer (Bertin Technologies) and Qiagen RNeasy Mini Kits according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

value: Heart tissue


title: SLL_12

status: Public on Mar 21 2012

type: RNA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

description: Liver tissue from mice that fasted for 48 hours.

hyb_protocol: standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.

data_processing: Data was extracted using the Illumina GenomeStudio software(v1.1.1).  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores will be included in the supplemental file.

label: Streptavidin-Cy3 bound to biotin-labeled cRNA.

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus liver tissue

label_protocol: standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol: RNA was extracted from liver tissue using 1.0mm glass beads (BioSpec Products, Inc.) in a Precellys 24 Tissue Homogenizer (Bertin Technologies) and Qiagen RNeasy Mini Kits according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

tag: tissue

value: Liver tissue

tag: strain

value: Balb-c mice

tag: treatment

value: fasted for 48 hours


title: SNL_2

treatment_protocol: Liver tissue from mice that fasted for 48 hours.


title: CLH_26

treatment_protocol: Heart tissue from mice that were fed an ad lib diet.

value: fed an ad lib diet


title: SRL_7


title: SLH_11

description: Heart tissue from mice that fasted for 48 hours.


title: SNH_1

treatment_protocol: Heart tissue from mice that fasted for 48 hours.


title: CNH_16


title: SRH_6


title: OV90 P3 2

status: Public on Mar 12 2012

description:
This paclitaxel resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles.  For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 6 cycles.  Subclones were isolated and expanded after the last cycle.
OV90 P3 2

hyb_protocol: standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Human Ref-8 v23 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~22,000 transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina BeadStudio software(v1.5.0.34). Any spots at or below the background were filtered out using an Illumina detection value below 0.98. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores will be included in the supplemental file.

organism: Homo sapiens

source_name: The ovarian cancer cell line OV90 was obtained from The American Type Culture Collection (ATCC)

extract_protocol: RNA was extracted from the treated cells using Trizol. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: Cells were grown in 1:1 mixture of MCDB 105 medium (Sigma) and Medium 199 (Invitrogen) containing 15% bovine serum and antibiotics (100 units/ml penicillin and 100 ug/ml streptomycin) at 37°C in a humidified atmosphere of 5% CO2, these untreated cells were then harvested for RNA preparation.

tag: cell type

value: ovarian cancer cell

tag: cell line

tag: resistance type


title: OV901 CA 1

description:
This cisplatin resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles.  For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 4 cycles.  Subclones were isolated and expanded after the last cycle.
OV901 CA 1

hyb_protocol: standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Human Ref-8 v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~22,000 transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.


title: OV90 P7 2

description:
This paclitaxel resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles.  For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 6 cycles.  Subclones were isolated and expanded after the last cycle.
OV90 P7 2


title: OV90 D7 2

description:
This doxorubicin resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles.  For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 4 cycles.  Subclones were isolated and expanded after the last cycle.
OV90 D7 2


title: OV90 D6 2

description:
This doxorubicin resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles.  For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 4 cycles.  Subclones were isolated and expanded after the last cycle.
OV90 D6 2


title: OV90 P3 1

description:
This paclitaxel resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles.  For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 6 cycles.  Subclones were isolated and expanded after the last cycle.
OV90 P3 1


title: OV901 CA 2

description:
This cisplatin resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles.  For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 4 cycles.  Subclones were isolated and expanded after the last cycle.
OV901 CA 2


title: OV901 CD 1

description:
This cisplatin resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles.  For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 4 cycles.  Subclones were isolated and expanded after the last cycle.
OV901 CD 1


title: OV901 CD 2

description:
This cisplatin resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles.  For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 4 cycles.  Subclones were isolated and expanded after the last cycle.
OV901 CD 2


title: OV90 D7 1

description:
This doxorubicin resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles.  For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 4 cycles.  Subclones were isolated and expanded after the last cycle.
OV90 D7 1


title: OV90 P7 1

description:
This paclitaxel resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles.  For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 6 cycles.  Subclones were isolated and expanded after the last cycle.
OV90 P7 1


title: OV90 2

description:
ovarian cancer cell line derived from the ascites of a patient with grade 3, stage IIIC malignant papillary serous adenocarcinoma
OV90 2


title: OV90 1

description:
ovarian cancer cell line derived from the ascites of a patient with grade 3, stage IIIC malignant papillary serous adenocarcinoma
OV90 1


title: IL-6 1a

status: Public on Jan 05 2012

hyb_protocol: Microarray hybridization was performed for 16 hours using 750 ng of biotin labeled cRNA on a human Ref-8 v2 Expression BeadChip containing 22,000 clones (Illumina). The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina BeadStudio software(v1). Any spots at or below the background were filtered out using an Illumina detection score of 0.98 and below. The natural log of  all remaining genes were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores will be included in the supplemental file.

growth_protocol: HepG2 human hepatocarcinoma cell line (American Type Culture Collection) were routinely grown and maintained in Minimum Eagle's medium (MEM)/F12 (1:1) supplemented with 10% heat-inactivated fetal bovine serum, 50 units/ml penicillin and 50 ug/ml streptomycin under standard cell culture conditions at 37°C and 5% CO2 in a humid environment.

extract_protocol: Total RNA was extracted from HepG2 cells using RNeasy plus mini kit (Qiagen), and its quality was assessed using an Agilent BioAnalyzer (Agilent Technologies) with RNA 6000 nano chips.

treatment_protocol: HepG2 human hepatocarcinoma cells were seeded in 35- or 60-mm dishes and grown as above to ~90% confluence after which they were serum starved for 4 hr followed by the addition of vehicle, IL-6 (20 ng/ml) for 1 hr, followed by RNA Isolation.


title: IL-6 4b

source_name: HepG2 human hepatocarcinoma cell line (American Type Culture Collection)

treatment_protocol: HepG2 human hepatocarcinoma cells were seeded in 35- or 60-mm dishes and grown as above to ~90% confluence after which they were serum starved for 4 hr followed by the addition of vehicle, IL-6 (20 ng/ml) for 4 hr, followed by RNA Isolation.


title: IL-6 8a

treatment_protocol: HepG2 human hepatocarcinoma cells were seeded in 35- or 60-mm dishes and grown as above to ~90% confluence after which they were serum starved for 4 hr followed by the addition of vehicle, IL-6 (20 ng/ml) for 8 hr, followed by RNA Isolation.


title: IL-6 1b


title: IL-6 2b

treatment_protocol: HepG2 human hepatocarcinoma cells were seeded in 35- or 60-mm dishes and grown as above to ~90% confluence after which they were serum starved for 4 hr followed by the addition of vehicle, IL-6 (20 ng/ml) for 2 hr, followed by RNA Isolation.


title: IL-6 4a


title: IL-6 8b


title: PDTC 4b

treatment_protocol: HepG2 human hepatocarcinoma cells were seeded in 35- or 60-mm dishes and grown as above to ~90% confluence after which they were serum starved for 4 hr followed by the addition of vehicle, PDTC (50 µM) for 4 hr, followed by RNA Isolation.


title: PDTC 4a


title: IL-6 2a


title: IL-6 vehicle_a

treatment_protocol: HepG2 human hepatocarcinoma cells were seeded in 35- or 60-mm dishes and grown as above to ~90% confluence after which they were serum starved for 4 hr followed by RNA Isolation.


title: IL-6 vehicle_b


title: PDTC 8b

treatment_protocol: HepG2 human hepatocarcinoma cells were seeded in 35- or 60-mm dishes and grown as above to ~90% confluence after which they were serum starved for 4 hr followed by the addition of vehicle, PDTC (50 µM) for 8 hr, followed by RNA Isolation.


title: OV90 D6 1

description:
This doxorubicin resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles.  For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 4 cycles.  Subclones were isolated and expanded after the last cycle.
OV90 D6 1


title: PDTC 8a


title: PDTC 2a

treatment_protocol: HepG2 human hepatocarcinoma cells were seeded in 35- or 60-mm dishes and grown as above to ~90% confluence after which they were serum starved for 4 hr followed by the addition of vehicle, PDTC (50 µM) for 2 hr, followed by RNA Isolation.


title: PDTC 1b

treatment_protocol: HepG2 human hepatocarcinoma cells were seeded in 35- or 60-mm dishes and grown as above to ~90% confluence after which they were serum starved for 4 hr followed by the addition of vehicle, PDTC (50 µM) for 1 hr, followed by RNA Isolation.


title: PDTC 2b


title: PDTC vehicle_a


title: 3xTg-CTX-Vehicle-3

status: Public on Dec 31 2011

description: = Cortex from male 3xTgAD mice, 18 months of age,

hyb_protocol: standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's SentrixMouse Ref-8,v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina GenomeStudio software(v1.1.1). Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection p-values is included in the supplemental file.

source_name: Cortex

extract_protocol: The RNA purification was done using glass bead disruption followed by the RNEasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. The RNA was examined for quantity and quality using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Male 3xTgAD mice, 14 months of age, were maintained on a 12hr light dark cycle in pathogen free conditions. Animals received food and plain water ad libitum.

value: Cortex

tag: gender

value: male

tag: genotype/variation

tag: age

value: 18 months


title: PDTC 1a


title: 3xTg-CTX-Vehicle-1

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.


title: 3xTg-HIP-Vehicle-3

description: = Hippocampus from male 3xTgAD mice, 18 months of age,

data_processing: Data was extracted using the Illumina BeadStudio software(v3.4). Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection p-values is included in the supplemental file.

source_name: Hippocampus

value: Hippocampus


title: 3xTg-CTX-AMI-1

treatment_protocol: Male 3xTgAD mice, 14 months of age, were maintained on a 12hr light dark cycle in pathogen free conditions. Animals received food and water ad libitum. The test group received 100ug/g body weight amitriptyline-hydrochloride per os in their drinking water (Sigma-Aldrich, St. Louis MO) for 4 months.


title: PDTC vehicle_b


title: 3xTg-CTX-AMI-3


title: 3xTg-CTX-AMI-2


title: 3xTg-HIP-AMI-1


title: 3xTg-HIP-Vehicle-1


title: 3xTg-CTX-Vehicle-2


title: 3xTg-HIP-AMI-3


title: 3xTg-HIP-AMI-2


title: D5_KD_b

status: Public on Sep 22 2011

description: primary cortical neurons (Day 1) treated and grown to Day 5

hyb_protocol: standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Rat Ref-12 v1 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~22,000 transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina GenomeStudio software(v1.1.1) Any spots at or below the background were filtered out using an Illumina detection p-value above 0.02 The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores be included in Series supplementary file.

organism: Rattus norvegicus

source_name: Primary cortical neurons (Day 5) after 6 hour treatment with CHD5 KD shRNA sequences.

extract_protocol: RNA was isolated using RNeasy Kit (Qiagen). Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: CHD5 KD shRNA sequences were designed according to the instructions for the pLKO.1 system (Addgene).  Virus was packaged using HEK-293T cells, pLKO.1 vector with shRNA inserts for CHD5.   48 hours after transfection of 293 cells, medium containing virus was filtered (0.45 micron), then applied for 6 hours to primary cortical neurons one day after the neurons were plated (Day 1). Medium was removed, and replaced with Neural Basal Medium, and the cells were cultured until Day5 after which they were harvested for RNA preparation.

value: primary cortical neurons (Day 1)


title: D9_C_c

description: primary cortical neurons (Day 1) treated and grown to Day 9

source_name: Primary cortical neurons (Day 9) after 6 hour treatment with control shRNA sequences.

treatment_protocol: Control was as described (Sci307-1098,2005) Scramble, clone 1864 from Addgene, and used according to the instructions for the pLKO.1 system (Addgene). ). Virus was packaged using HEK-293T cells, pLKO.1 vector with shRNA inserts for the control.   48 hours after transfection of 293 cells, medium containing virus was filtered (0.45 micron), then applied for 6 hours to primary cortical neurons one day after the neurons were plated (Day 1). Medium was removed, and replaced with Neural Basal Medium, and the cells were cultured until Day9,  after which they were harvested for RNA isolation.


title: D9_KD_a

source_name: Primary cortical neurons (Day 9) after 6 hour treatment with CHD5 KD shRNA sequences.

treatment_protocol: CHD5 KD shRNA sequences were designed according to the instructions for the pLKO.1 system (Addgene).  Virus was packaged using HEK-293T cells, pLKO.1 vector with shRNA inserts for CHD5.   48 hours after transfection of 293 cells, medium containing virus was filtered (0.45 micron), then applied for 6 hours to primary cortical neurons one day after the neurons were plated (Day 1). Medium was removed, and replaced with Neural Basal Medium, and the cells were cultured until Day9 after which they were harvested for RNA preparation.


title: D9_C_a


title: D9_C_b


title: D5_C_b

source_name: Primary cortical neurons (Day 5) after 6 hour treatment with control shRNA sequences.

treatment_protocol: Control was as described (Sci307-1098,2005) Scramble, clone 1864 from Addgene, and used according to the instructions for the pLKO.1 system (Addgene). ). Virus was packaged using HEK-293T cells, pLKO.1 vector with shRNA inserts for the control.   48 hours after transfection of 293 cells, medium containing virus was filtered (0.45 micron), then applied for 6 hours to primary cortical neurons one day after the neurons were plated (Day 1). Medium was removed, and replaced with Neural Basal Medium, and the cells were cultured until Day5,  after which they were harvested for RNA isolation.


title: D12_KD_b

description: primary cortical neurons (Day 1) treated and grown to Day 12

source_name: Primary cortical neurons (Day 12) after 6 hour treatment with CHD5 KD shRNA sequences.

treatment_protocol: CHD5 KD shRNA sequences were designed according to the instructions for the pLKO.1 system (Addgene).  Virus was packaged using HEK-293T cells, pLKO.1 vector with shRNA inserts for CHD5.   48 hours after transfection of 293 cells, medium containing virus was filtered (0.45 micron), then applied for 6 hours to primary cortical neurons one day after the neurons were plated (Day 1). Medium was removed, and replaced with Neural Basal Medium, and the cells were cultured until Day12. after which they were harvested for RNA preparation.


title: 3xTg-HIP-Vehicle-2


title: D5_KD_c


title: D5_C_c


title: D5_KD_a


title: D12_KD_c


title: D9_KD_c


title: D9_KD_b


title: D12_C_c

source_name: Primary cortical neurons (Day 12) after 6 hour treatment with control shRNA sequences.

treatment_protocol: Control was as described (Sci307-1098,2005) Scramble, clone 1864 from Addgene, and used according to the instructions for the pLKO.1 system (Addgene). ). Virus was packaged using HEK-293T cells, pLKO.1 vector with shRNA inserts for the control.   48 hours after transfection of 293 cells, medium containing virus was filtered (0.45 micron), then applied for 6 hours to primary cortical neurons one day after the neurons were plated (Day 1). Medium was removed, and replaced with Neural Basal Medium, and the cells were cultured until Day12,  after which they were harvested for RNA isolation.


title: D12_C_b


title: D12_KD_a


title: D12_C_a


title: CLL_27

description: Liver tissue from mice that were fed an ad lib diet.


title: SD-3

status: Public on Aug 18 2011

hyb_protocol: standard Illumina protocol. In short, a total of 0.75?g of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina BeadStudio software(v1). Any spots at or below the background were filtered out using an Illumina detection p-value score of 0.02 and above. The natural log of  all remaining genes were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores will be included in the supplemental files.

extract_protocol: RNA was extracted using Qiagen RNAeasy Mini kit

treatment_protocol: Starting at 56 weeks of age, fed a standard AIN-93G dirt, (SD).

value: C57BL/6J, Gender:Male, Tissue:Liver, Age:82weeks


title: HFD-3

treatment_protocol: Starting at 56 weeks of age, fed a high-fat diet (HFD).


title: HFD-H-2

treatment_protocol: Starting at 56 weeks of age, fed a high-fat diet plus100mg/kg SRT1720 (HFD-H).


title: HFD-1


title: SD-1


title: YI-KO-2

status: Public on Aug 04 2011

description: Liver tissue, C57B/6J mINDY(-/-) knockout

data_processing: Data was extracted using the Illumina BeadStudio software(v3.4.0).  Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores will be included in the supplemental file.

value: Liver

value: 3 month old

value: mINDY(-/-) knockout


title: HFD-L-1

treatment_protocol: Starting at 56 weeks of age, fed a high-fat diet plus 30mg/kg SRT1720 (HFD-L).


title: YI-WT-5

description: Liver tissue, C57B/6J Wt

value: Wt


title: YI-KO-10


title: HFD-H-1


title: SD-2


title: HFD-L-3


title: YI-WT-9

description: Liver tissue, C57B/6J Wt


title: SNT_3

description: Subcutaneous 4T1 breast cancer tumor mass from mice that were fasted for 48 hours.

source_name: 4T1-luc murine breast cancer cells were purchased from SibTech (Brookfield, CT).

extract_protocol: RNA was extracted from a subcutaneous 4T1 breast cancer tumor mass using 1.0mm glass beads (BioSpec Products, Inc.) in a Precellys 24 Tissue Homogenizer (Bertin Technologies) and Qiagen RNeasy Mini Kits according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

value: Subcutaneous 4T1 breast cancer tumor mass tissue


title: HFD-H-3


title: HFD-L-2


title: HFD-2


title: YI-KO-4


title: YI-WT-3

description: Liver tissue, C57B/6J Wt


title: YI-KO-6


title: Cervical tumor biopsy, P-322

status: Public on Jul 19 2011

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

description:
P-322
Validation cohort

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0

label: biotin

source_name: Cervical tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: 1-4 tumor samples wer collected from each patient at the time of diagnosis

extract_protocol: RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. RNA from different biopsies of the same tumor was pooled. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80 C until used for analysis. Biopsies with more than 50% tumor cells in HE stained sections from the central part of the specimen were used further.

tag: histology

value: Squamous cell carcinoma

tag: gene-based hypoxia

value: More hypoxic

tag: imaging-based hypoxia

tag: combined hypoxia biomarker

tag: cohort (gse36562 study)

value: Validation cohort

tag: hypoxia score

value: High

value: cervical tumor

tag: figo stage

tag: cohort

tag: cohort (gse38964 study)

tag: 3p status

value: Not determined


title: YI-KO-8

tag: tissue

tag: strain


title: YI-WT-1

description: Liver tissue, C57B/6J Wt


title: Cervical tumor biopsy, P-319

description:
P-319
Validation cohort

value: Less hypoxic

value: Low


title: YI-WT-7

description: Liver tissue, C57B/6J Wt


title: Cervical tumor biopsy, P-318

description:
P-318
Validation cohort


title: Cervical tumor biopsy, P-292

description:
Basic cohort
P-292

value: basic cohort

tag: lymph node status (gse38433 study)


title: Cervical tumor biopsy, P-293

description:
Basic cohort
P-293


title: Cervical tumor biopsy, P-274

description:
Basic cohort
P-274


title: Cervical tumor biopsy, P-276

description:
Basic cohort
P-276


title: Cervical tumor biopsy, P-270

description:
Basic cohort
P-270


title: Cervical tumor biopsy, P-289

description:
Basic cohort
P-289


title: Cervical tumor biopsy, P-291

description:
Basic cohort
P-291


title: Cervical tumor biopsy, P-232

description:
Basic cohort
P-232


title: Cervical tumor biopsy, P-257

description:
Basic cohort
P-257


title: Cervical tumor biopsy, P-285

description:
Basic cohort
P-285


title: Cervical tumor biopsy, P-275

description:
P-275
Validation cohort


title: Cervical tumor biopsy, P-251

description:
Basic cohort
P-251


title: Cervical tumor biopsy, P-067

description:
Basic cohort
P-067

value: DCE-MRI cohort


title: Cervical tumor biopsy, P-200

description:
Basic cohort
P-200

hyb_protocol: The samples were hybridized to the arrays at 58oC overnight, using the standard Illumina hybridization protocol.

scan_protocol: Scanning was performed with an Illumina BeadArray reader, using the standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization in J-Express.

source_name: Cervical tumor, 2B

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

growth_protocol: 1-4 tumor samples were collected from each patient at the time of diagnosis.

extract_protocol: RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. RNA from different biopsies of the same tumor was pooled. Quality control was performed with the Agilent Bioanalyzer.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80oC until used for analysis. Biopsies with more than 50% tumor cells in HE stained sections from the central part of the specimen were used further.

value: Integrative cohort

value: Loss


title: Cervical tumor biopsy, P-252

description:
Basic cohort
P-252


title: Cervical tumor biopsy, P-246

description:
Basic cohort
P-246


title: Cervical tumor biopsy, P-247

description:
Basic cohort
P-247


title: Cervical tumor biopsy, P-199

description:
Basic cohort
P-199

value: No loss


title: Cervical tumor biopsy, P-203

description:
Basic cohort
P-203


title: Cervical tumor biopsy, P-221

description:
P-221
Validation cohort


title: Cervical tumor biopsy, P-208

description:
P-208
Validation cohort


title: Cervical tumor biopsy, P-261

description:
Basic cohort
P-261


title: D5_C_a

value: primary cortical neurons (Day 1)


title: Cervical tumor biopsy, P-202

description:
Basic cohort
P-202

source_name: Cervical tumor, 1B2


title: Cervical tumor biopsy, P-265

description:
Basic cohort
P-265


title: Cervical tumor biopsy, P-058

description:
Basic cohort
P-058


title: Cervical tumor biopsy, P-210

description:
Basic cohort
P-210


title: Cervical tumor biopsy, P-220

description:
Basic cohort
P-220


title: Cervical tumor biopsy, P-198

description:
P-198
Validation cohort


title: Cervical tumor biopsy, P-193

description:
Basic cohort
P-193

source_name: Cervical tumor, 1B1


title: Cervical tumor biopsy, P-195

description:
Basic cohort
P-195


title: Cervical tumor biopsy, P-194

description:
Basic cohort
P-194

source_name: Cervical tumor, 3B


title: Cervical tumor biopsy, P-197

description:
Basic cohort
P-197

source_name: Cervical tumor, 2A


title: Cervical tumor biopsy, P-180

description:
Basic cohort
P-180


title: Cervical tumor biopsy, P-169

description:
Basic cohort
P-169


title: Cervical tumor biopsy, P-196

description:
P-196
Validation cohort


title: Cervical tumor biopsy, P-192

description:
Basic cohort
P-192


title: Cervical tumor biopsy, P-189

description:
Basic cohort
P-189


title: Cervical tumor biopsy, P-177

description:
Basic cohort
P-177


title: Cervical tumor biopsy, P-162

description:
Basic cohort
P-162


title: Cervical tumor biopsy, P-182

description:
Basic cohort
P-182


title: Cervical tumor biopsy, P-136

description:
Basic cohort
P-136


title: Cervical tumor biopsy, P-091

description:
Basic cohort
P-091


title: Cervical tumor biopsy, P-191

description:
Basic cohort
P-191


title: Cervical tumor biopsy, P-121

description:
Basic cohort
P-121


title: Cervical tumor biopsy, P-092

description:
Basic cohort
P-092


title: Cervical tumor biopsy, P-172

description:
Basic cohort
P-172


title: Cervical tumor biopsy, P-130

description:
Basic cohort
P-130


title: Cervical tumor biopsy, P-129

description:
Basic cohort
P-129


title: Cervical tumor biopsy, P-124

description:
Basic cohort
P-124

source_name: Cervical tumor, 3A


title: Cervical tumor biopsy, P-133

description:
Basic cohort
P-133


title: Cervical tumor biopsy, P-141

description:
Basic cohort
P-141


title: Cervical tumor biopsy, P-126

description:
Basic cohort
P-126


title: Cervical tumor biopsy, P-146

description:
Basic cohort
P-146


title: Cervical tumor biopsy, P-096

description:
Basic cohort
P-096


title: Cervical tumor biopsy, P-138

description:
Basic cohort
P-138


title: Cervical tumor biopsy, P-101

description:
Basic cohort
P-101


title: Cervical tumor biopsy, P-098

description:
Basic cohort
P-098


title: Cervical tumor biopsy, P-087

description:
Basic cohort
P-087


title: Cervical tumor biopsy, P-093

description:
Basic cohort
P-093


title: Cervical tumor biopsy, P-084

description:
Basic cohort
P-084


title: Cervical tumor biopsy, P-080

description:
Basic cohort
P-080


title: Cervical tumor biopsy, P-078

description:
Basic cohort
P-078

source_name: Cervical tumor, 4A


title: Cervical tumor biopsy, P-074

description:
Basic cohort
P-074


title: Cervical tumor biopsy, P-068

description:
Basic cohort
P-068


title: Cervical tumor biopsy, P-073

description:
Basic cohort
P-073


title: Cervical tumor biopsy, P-032

description:
Basic cohort
P-032


title: Input

status: Public on Mar 01 2011

type: SRA

description: Negative control- input DNA, no immunoprecipitation

library_source: genomic

data_processing:
Alignment: The first 35 bases were aligned to the mouse mm9 genome using the Illumina Genome Analysis Pipeline v1.3.
Peaks: Peak detection was performed using CisGenome, 2 sample anaylsis, input as negative control, FDR 0.1, window size 100, boundary refinement and single strand filtering performed.

molecule: genomic DNA

growth_protocol:
Naïve CD4+ T cells were purified to 95% purity from the spleens and lymph nodes of 4-6 week old Balb/c mice (Taconic) using CD4+CD62L+ T cell Purification Kit II per manufacturer’s instructions (Miltenyi).
Th1 cells: Naive, purified CD4+CD62L+ T cells cells were plated onto anti-CD3 (1μg/ml), anti-CD28 (2 μg/ml) coated plates at 1-2 x 106/ml in the presence of 1ng/ml IL-12, 10μg/ml anti-IL-4. IL-2 (100U/ml) was added 24 hours later.  Cultures were expanded in IL-2 (100U/ml) three days after initial culture.
Th2 cells: purified CD4+CD62L+ T cells cells were plated onto anti-CD3 (1μg/ml), anti-CD28 (2 μg/ml) coated plates at 1-2 x 106/ml in the presence of 10ng/ml IL-4, 10μg /ml anti-IFNγ. IL-2 (100U/ml) was added 24 hours later.  Cultures were expanded in IL-2 (100U/ml) three days after initial culture.
Th17 cells: Th17 cells were cultured using soluble anti-CD3 (4μg/ml), soluble anti-CD28 (1μg/ml), 10μg /ml both anti-IL-4 and anti-IFNγ, 100 ng/ml IL-6, 10ng/ml IL-1β and 1ng/ml TGF-β.  The Th17 cultures were expanded in the presence of 10ng/ml IL-23 after three days.

extract_protocol: Cells were crosslinked with formaldehyde, nuclei were treated with MNase, and sonicated with a bath sonicator (Bioruptor).  BRG1-DNA complexes were isolated with antibody.  The enriched DNA fragments or the sheared genomic DNA fragments (Input) were modified to construct a sequencing library according to the manufacturer’s protocol (Illumina/Solexa, San Diego, CA) with some modifications.  Briefly, the ends of the fragments were repaired using T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase), and T4 polynucleotide kinase (PNK) and A’s were added to the 3’ end.  Adapters were ligated to the DNA fragments and a 18-cycle PCR amplification was performed before size selection (250-300 bases) on a 2% agarose gel, followed by cluster generation and sequencing with Solexa/Illumina Genome Analyzer (GA-II).

treatment_protocol: Stimulated cells: Effector cells were stimulated with PMA (50ng/ml) and Ionomycin (500ng/ml) for 1.5 hours.

value: Balb/C

tag: cell type

value: CD4+ T helper cells, pooled

tag: passages

tag: chip antibody


title: Cervical tumor biopsy, P-063

description:
Basic cohort
P-063


title: Th1S

description: Chromatin IP against BRG1

source_name: Chromatin IP against BRG1, stimulated Th1

value: Th1 Stimulated CD4+ T helper cells

value: differentiated in culture, single round, from Naïve cells

value: BRG (J1 antibody described in Genes Dev. 1996 Sep 1;10(17):2117-30, PubMed ID:8804307)


title: Th17S

description: Chromatin IP against BRG1

source_name: Chromatin IP against BRG1, stimulated Th17

value: Th17 Stimulated CD4+ T helper cells


title: Cervical tumor biopsy, P-002

description:
P-002
Validation cohort

value: Squamous cell carcinoma

value: More hypoxic

value: High

value: Validation cohort


title: Cervical tumor biopsy, P-005

description:
Basic cohort
P-005

value: Less hypoxic

value: Low

value: cervical tumor


title: Cervical tumor biopsy, P-053

description:
Basic cohort
P-053

value: DCE-MRI cohort

value: basic cohort

value: Integrative cohort


title: Cervical tumor biopsy, P-055

description:
Basic cohort
P-055

value: Loss


title: Th2S

description: Chromatin IP against BRG1

source_name: Chromatin IP against BRG1, stimulated Th2

value: Balb/C

value: Th2 Stimulated CD4+ T helper cells


title: Cervical tumor biopsy, P-072

description:
Basic cohort
P-072

value: No loss


title: Cervical tumor biopsy, P-308

description:
P-308
Validation cohort

value: Not determined


title: Cervical tumor biopsy, P-018

description:
Basic cohort
P-018


title: Cervical tumor biopsy, P-222

description:
Basic cohort
P-222


title: Th_KO-1

status: Public on Jun 24 2011

description:
Klf4fl/fl mice (Katz et al., 2002) were crossed with CD4-Cre mice (Lee et al., 2001) to generate Klf4fl/flCD4Cre+(KO) mice.
Freshly isolated DP+SP4 thymocytes from KO mice.

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's SentrixMouse Ref-8, v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina GenomeStudio software (v2010.1). Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection p-values is included in the data table.

label: Biotin

source_name: Freshly isolated DP+SP4 thymocytes, KO mice

label_protocol: Standard Illumina protocol using the Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791). In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double-stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol: Total RNA was extracted from the freshly isolated DP+SP4 thymocytes using the RNeasy Mini kit (Qiagen). The quality and quantity of total RNA were analyzed by the Agilent 2100 Bioanalyzer using RNA 6000 nano chips (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Thymus were isolated from KO mice and single-cell suspensions were prepared. CD4+ T cells were enriched with a CD4 T Cell Isolation Kit either from Miltenyi Biotec (Auburn, CA) or from Stem Cell Technologies (Vancouver, BC) according to the manufacturer's’ instructions. The purity of these isolated cells was >94%.

tag: strain/background

tag: genotype

value: Klf4fl/fl-CD4-Cre+ (Klf4 conditional KO)

value: thymus

value: DP+SP4 thymocytes

tag: age

value: 8-10 weeks


title: uNaive

description: Chromatin IP against BRG1

source_name: Chromatin IP against BRG1, uNaive

value: Naive CD4+ T helper cells, straight from mouse

value: CD4+CD62L+ Naive cells from 4-6 week mice, spleens and lymph nodes

value: BRG (J1 antibody described in Genes Dev. 1996 Sep 1;10(17):2117-30, PubMed ID:8804307)


title: uTh1

description: Chromatin IP against BRG1

source_name: Chromatin IP against BRG1, resting Th1

value: resting Th1 CD4+ T helper cells

value: differentiated in culture, single round, from Naïve cells


title: Th_WT-1

description:
Klf4fl/fl mice (Katz et al., 2002) were crossed with CD4-Cre mice (Lee et al., 2001) to generate Klf4fl/flCD4Cre+(KO) mice.
Freshly isolated DP+SP4 thymocytes from control mice.

source_name: Freshly isolated DP+SP4 thymocytes, control mice

treatment_protocol: Thymus were isolated from control mice and single-cell suspensions were prepared. CD4+ T cells were enriched with a CD4 T Cell Isolation Kit either from Miltenyi Biotec (Auburn, CA) or from Stem Cell Technologies (Vancouver, BC) according to the manufacturer's’ instructions. The purity of these isolated cells was >94%.

value: Klf4fl/fl-CD4-Cre- (control)


title: Th_WT-3


title: Th_KO-3


title: IC4

description:
The BEAS-2B cell line is derived from human tracheal epithelium transformed by an adenovirus 12-SV40 hybrid virus (28) (ATCC, Manassas, VA).  Cell cultures were maintained in F12/DMEM (Gibco/Invitrogen, Frederick, MD) containing 5% heat-inactivated fetal calf serum, 2 mM L-glutamine, penicillin (100 U/ml) and streptomycin (100 mg/ml) (29).  Cells were cultured at 37°C in humidified air containing 5% CO2. BEAS-2B cells were used from passages 36 to 45.
Collection of control transcripts obtained by immunoprecipitation of mRNA complexes with a mouse IgG.

hyb_protocol: standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix HumanRef-8,v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina BeadStudio software(v3.4.0). Any spots at or below the background were filtered out using an Illumina detection p-value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores will be included in the supplemental files.

source_name: The human BEAS-2B cell line is derived from tracheal epithelium transformed by an adenovirus 12-SV40 hybrid virus (ATCC, Manassas, VA).

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of IP-RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol: RNA was extracted by the addition of acid phenol-chloroform (Ambion), to the bead supernatant followed by the addition of 3M sodium acetate, pH 5.2 (10% v/v) and precipitation with ethanol.  Quality and quantity of the IP-RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: BEAS-2B cells were grown to 85% confluence and lysed by the addition of PLB supplemented with RNAse inhibitor (10 U/µl final concentration, New England Biolabs) and protease inhibitors (Complete Mini, EDTA-free, Roche) as described (25).  For isolation of GR-associated transcripts, cytoplasmic lysates obtained from 1.6x107 cells/condition were generated as described (25) and verified to be  free of nuclear contamination by Western blot analysis of cytoplasmic (beta-tubulin, Santa Cruz Biotechnology) and nuclear proteins (PCNA, HNRNP C1/C2, Santa Cruz Biotechnology).  Cytoplasmic lysates were mixed with protein A sepharose beads (Sigma) coated with 30 µg of rabbit IgG.  Beads were washed three times with NT2 buffer (50 mM Tris-HCl [pH 7.4], 150 mM NaCl2, 1 mM MgCl2, and 0.05% Nonidet P-40), incubated with 20 U of RNase-free DNase I (15 min at 30°C), and further incubated in 100 µl NT2 buffer containing 0.1% SDS and 0.5 mg/ml proteinase K (30 min at 55°C).

tag: cell line

tag: antibody

value: rabbit IgG

tag: antibody manufacturer

value: Santa Cruz Biotechnolog

tag: antibody catalog #


title: Th_KO-2


title: Th_WT-2


title: IC2


title: GR4

description:
The BEAS-2B cell line is derived from human tracheal epithelium transformed by an adenovirus 12-SV40 hybrid virus (28) (ATCC, Manassas, VA).  Cell cultures were maintained in F12/DMEM (Gibco/Invitrogen, Frederick, MD) containing 5% heat-inactivated fetal calf serum, 2 mM L-glutamine, penicillin (100 U/ml) and streptomycin (100 mg/ml) (29).  Cells were cultured at 37°C in humidified air containing 5% CO2. BEAS-2B cells were used from passages 36 to 45.
Collection of transcripts associated with glucocorticoid receptor, obtained by immunoprecipitation of GR-mRNA complexes

treatment_protocol: BEAS-2B cells were grown to 85% confluence and lysed by the addition of PLB supplemented with RNAse inhibitor (10 U/µl final concentration, New England Biolabs) and protease inhibitors (Complete Mini, EDTA-free, Roche).  For isolation of GR-associated transcripts, cytoplasmic lysates obtained from 1.6x107 cells/condition were generated as described and verified to be  free of nuclear contamination by Western blot analysis of cytoplasmic (beta-tubulin, Santa Cruz Biotechnology) and nuclear proteins (PCNA, HNRNP C1/C2, Santa Cruz Biotechnology).  Cytoplasmic lysates were mixed with protein A sepharose beads (Sigma) coated with 30 µg of a specific GR antibody (H-300 clone).  Beads were washed three times with NT2 buffer (50 mM Tris-HCl [pH 7.4], 150 mM NaCl2, 1 mM MgCl2, and 0.05% Nonidet P-40), incubated with 20 U of RNase-free DNase I (15 min at 30°C), and further incubated in 100 µl NT2 buffer containing 0.1% SDS and 0.5 mg/ml proteinase K (30 min at 55°C).

value: anti-GR2 H-300


title: IC1


title: uTh2

description: Chromatin IP against BRG1

source_name: Chromatin IP against BRG1, resting Th2

value: Balb/C

value: resting Th2 CD4+ T helper cells


title: GR3


title: GR2


title: HMEC/CONTROL-1

status: Public on Dec 25 2010

description: Primary Human Mammalian Epithelial Cells (HMECs) were cultured in HMEC medium in the prescence of 15% control serum for 6 hours

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Human HT-12, v3 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip targets more than 25,000 annotated genes with more than 48,000 probes. Probes were designed using the RefSeq (Build 36.2, Rel 22) and the UniGene (Build 199) databases with an average of 15-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina BeadStudio software(v3.0). Any spots at or below the background were filtered out using an Illumina detection p-value of 0.02 and above. The natural log of all remaining scores was used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores will be included in the supplemental file.

source_name: HMEC/CONTROL

growth_protocol: Cells were cultured in HMEC medium (ScienCell) at 37oC and 5% CO2 in Poly-L-Lysine coated culture dishes (Sigma).

extract_protocol: RNA was extracted from the serum treated cell cultures using TRI Reagent® (Ambion).  Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: Treatment consisted of HMEC cells being stimulated with HMEC basal medium containing 15% Control serum for 6 hours then cells were harvested and processed for RNA extraction.


title: ATM+/+ IR-1

status: Public on Jan 05 2011

description: B-lymphocyte cell line GM02184 (wild type, ATM +/+) was purchased from Coriell Cell Repositories and cultured in RPMI medium 1640 (Quality Biological Inc.) with 15% FBS and penicillin/streptomycin.  This cell line is normal for the checkpoint kinase ATM (Ataxia Telangiectasia Mutated).

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Human-HT12 v1 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~48,00 transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina BeadStudio Gene Expression software(v3.4.0). Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std. The sample quality was analyzed by scatter plot, principal component analysis (PCA), and gene sample z-scores based hierarchy clustering to exclude possible outliers. ANOVA test was used to eliminate the genes with larger variances within each comparison group.  Genes were considered to be significantly changed after calculating Z ratio, indicating fold difference (Z > 1.5 or < -1.5), false discovery rate (fdr), which controls for the expected proportion of false rejected hypothesis (fdr < or equal to 0.3) and p < 0.05.  Complete data including detection p-value is included in this file.

extract_protocol:
Immunoprecipitations (IP) of ribonucleoprotein (RNP) complexes followed by microarray analysis was performed as previously described. In short, lymphocytes were harvested in lysis buffer (150 mM KOAc, 2.5 mM Mg(OAc)2, 20 mM K-Hepes pH. 7.5, DTT, PMSF, RNasin and protease inhibitors) and 3 mg of protein were used for IP for 1 h at 4°C in the presence of excess antibody [30 ?g of either anti-HuR antibody (Santa Cruz Biotech.), or control immunoglobulin IgG (BD Pharmingen)]. After thorough washes with NT2 buffer (50 mM Tris-HCl [pH 7.4], 150 mM NaCl, 1 mM MgCl2, and 0.05% Nonidet P-40) beads were treated with 20 units of RNase-free DNase I (15 min at 37°C), and incubated (20 min, 55°C) in 100 µl NT2 buffer containing 0.1% SDS and 0.5 mg/ml Proteinase K.
RNA from IP material was extracted using phenol and chloroform method in the presence of GlycoBlue (Ambion).  The quality and quantity of total RNA were analyzed by Agilent 2100 Bioanalyzer using RNA 6000 nano chips (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Cells were exposed to 1 Gy of IR and lysed 6 h later.

value: wild type, ATM +/+

value: HuR

tag: vendor

value: Santa Cruz Biotech


title: HMEC/GHRD-6

description: Primary Human Mammalian Epithelial Cells (HMECs) were cultured in HMEC medium in the prescence of 15% GHRD serum for 6 hours

source_name: HMEC/GHRD

treatment_protocol: Treatment consisted of HMEC cells being stimulated with HMEC basal medium containing 15% GHRD serum for 6 hours then cells were harvested and processed for RNA extraction.


title: ATM-/- Ctrl-2

description: B-lymphocyte cell line GM03332 (AT, ATM -/-) was purchased from Coriell Cell Repositories and cultured in RPMI medium 1640 (Quality Biological Inc.) with 15% FBS and penicillin/streptomycin. This cell line is null for the checkpoint kinase ATM (Ataxia Telangiectasia Mutated).

treatment_protocol: Control cells were left untreated(no IR exposure) and lysed 6 h later.

value: AT, ATM -/-


title: ATM-/- Ctrl-3

source_name: B-lymphocyte cell line GM03332 (AT, ATM -/-)


title: ATM+/+ IR-2

source_name: B-lymphocyte cell line GM02184 (wild type, ATM +/+)


title: HMEC/CONTROL-5

value: Primary Human Mammalian Epithelial Cells (HMECs)


title: HMEC/CONTROL-3


title: ATM+/+ Ctrl-1


title: HMEC/CONTROL-2


title: HMEC/CONTROL-4


title: HMEC/GHRD-2


title: HMEC/GHRD-1


title: ATM-/- Ctrl-1


title: ATM+/+ IR-3


title: HMEC/GHRD-4


title: HMEC/GHRD-5


title: ATM+/+ Ctrl-3


title: ATM-/- IR-2


title: HMEC/GHRD-3


title: ATM+/+ Ctrl-2


title: ATM-/- IR-1


title: Cervical tumor biopsy, P-166

description:
Basic cohort
P-166

source_name: Cervical tumor, 2B

tag: histology

value: Squamous cell carcinoma

tag: gene-based hypoxia

value: Less hypoxic

tag: imaging-based hypoxia

tag: combined hypoxia biomarker

tag: cohort (gse36562 study)

value: DCE-MRI cohort

tag: hypoxia score

value: Low

value: cervical tumor

tag: figo stage

tag: cohort

value: basic cohort

value: Integrative cohort

value: Loss


title: Pulse IgM 9h-3

status: Public on May 24 2010

description: Pool of spleen B cells from 8-12 week-old C57BL/6J mice.

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix HumanRef-8,v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing: Data was extracted using the Illumina BeadStudio software(v3.0). Any spots at or below the background were filtered out using an Illumina detection p-value of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores are available in 'GSE20477_non-normalized.txt', which is linked to the Series GSE20477 record as a supplementary file.

source_name: C57BL/6J mouse spleen B lymphocytes, pulse IgM, 9h

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791). In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol: RNA was extracted from the B cells using Qiagen RNAeasy Mini kit. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.

treatment_protocol: Primary B lymphocytes were isolated using Auto-MACS (Miltenyi Biotec) by negative selection. B cells were stimulated with 10ug/ml anti-IgM at 4 degrees C for 30 minutes, the anti-IgM was washed out and then the cells were incubated in complete medium at 37 degrees C for 9 hr.

tag: strain

value: 8-12 weeks

tag: tissue

value: spleen

tag: cell type

value: pool of B cells


title: Pulse IgM 3h-2

source_name: C57BL/6J mouse spleen B lymphocytes, pulse IgM, 3h

treatment_protocol: Primary B lymphocytes were isolated using Auto-MACS (Miltenyi Biotec) by negative selection. B cells were stimulated with 10ug/ml anti-IgM at 4 degrees C for 30 minutes, the anti-IgM was washed out and then the cells were incubated in complete medium at 37 degrees C for 3 hr.

tag: age


title: Pulse IgM 6h-2

source_name: C57BL/6J mouse spleen B lymphocytes, pulse IgM, 6h

treatment_protocol: Primary B lymphocytes were isolated using Auto-MACS (Miltenyi Biotec) by negative selection. B cells were stimulated with 10ug/ml anti-IgM at 4 degrees C for 30 minutes, the anti-IgM was washed out and then the cells were incubated in complete medium at 37 degrees C for 6 hr.


title: Cont IgM 9h-3

source_name: C57BL/6J mouse spleen B lymphocytes, continuous IgM, 9h

treatment_protocol: Primary B lymphocytes were isolated using Auto-MACS (Miltenyi Biotec) by negative selection. B cells were stimulated with 10ug/ml anti-IgM at 4 degrees C for 30 minutes and then incubated at 37 degrees C for 9 hr.


title: Pulse IgM 6h-3


title: Pulse IgM 3h-3


title: Cont IgM 6h-3

source_name: C57BL/6J mouse spleen B lymphocytes, continuous IgM, 6h

treatment_protocol: Primary B lymphocytes were isolated using Auto-MACS (Miltenyi Biotec) by negative selection. B cells were stimulated with 10ug/ml anti-IgM at 4 degrees C for 30 minutes and then incubated at 37 degrees C for 6 hr.


title: Pulse IgM 9h-2


title: Pulse IgM 1h-2

source_name: C57BL/6J mouse spleen B lymphocytes, pulse IgM, 1h

treatment_protocol: Primary B lymphocytes were isolated using Auto-MACS (Miltenyi Biotec) by negative selection. B cells were stimulated with 10ug/ml anti-IgM at 4 degrees C for 30 minutes, the anti-IgM was washed out and then the cells were incubated in complete medium at 37 degrees C for 1 hr.


title: Pulse IgM 9h-1


title: Cont IgM 3h-3

source_name: C57BL/6J mouse spleen B lymphocytes, continuous IgM, 3h

treatment_protocol: Primary B lymphocytes were isolated using Auto-MACS (Miltenyi Biotec) by negative selection. B cells were stimulated with 10ug/ml anti-IgM at 4 degrees C for 30 minutes and then incubated at 37 degrees C for 3 hr.


title: Pulse IgM 0_5h-3

source_name: C57BL/6J mouse spleen B lymphocytes, pulse IgM, 0.5h

treatment_protocol: Primary B lymphocytes were isolated using Auto-MACS (Miltenyi Biotec) by negative selection. B cells were stimulated with 10ug/ml anti-IgM at 4 degrees C for 30 minutes, the anti-IgM was washed out and then the cells were incubated in complete medium at 37 degrees C for 30 minutes.


title: Pulse IgM 0_5h-2


title: Pulse IgM 1h-3


title: Cont IgM 3h-1


title: Cont IgM 6h-1


title: Pulse IgM 3h-1


title: Cont IgM 6h-2


title: Cont IgM 9h-2


title: Pulse IgM 1h-1


title: Pulse IgM 6h-1


title: Cont IgM 9h-1


title: Cont IgM 1h-3

source_name: C57BL/6J mouse spleen B lymphocytes, continuous IgM, 1h

treatment_protocol: Primary B lymphocytes were isolated using Auto-MACS (Miltenyi Biotec) by negative selection. B cells were stimulated with 10ug/ml anti-IgM at 4 degrees C for 30 minutes and then incubated at 37 degrees C for 1 hr.


title: Cont IgM 1h-1


title: Cont IgM 3h-2


title: Cont IgM 1h-2


title: Cont IgM 0_5h-3

source_name: C57BL/6J mouse spleen B lymphocytes, continuous IgM, 0.5h

treatment_protocol: Primary B lymphocytes were isolated using Auto-MACS (Miltenyi Biotec) by negative selection. B cells were stimulated with 10ug/ml anti-IgM at 4 degrees C for 30 minutes and then incubated at 37 degrees C for 30 minutes.


title: Pulse IgM 0_5h-1


title: Cont IgM 0_5h-2


title: IC3

source_name: The human BEAS-2B cell line is derived from tracheal epithelium transformed by an adenovirus 12-SV40 hybrid virus (ATCC, Manassas, VA).

tag: cell line

value: rabbit IgG

value: Santa Cruz Biotechnolog


title: 0h-1

source_name: C57BL/6J mouse spleen B lymphocytes

treatment_protocol: Primary B lymphocytes were isolated using Auto-MACS (Miltenyi Biotec) by negative selection. B cells were incubated at 4 degrees C for 30 minutes.


title: 0h-3


title: Cont IgM 0_5h-1


title: 0h-2


title: yeast-Fed-Batch-60 g/l ethanol-n°1

status: Public on Sep 01 2009

city: Toulouse

first: Laurent

last: Benbadis

address: 135 Av de Rangueil

country: France

institute: LISBP INSA CNRS UMR5504

description: Ethanol adaptation : all conditions detailed in Cot et al, (2007) FEMS Yeast Res. 7 : 22-32.

hyb_protocol: Prehybridisation was performed with solution of 1% BSA, 2 ×SSC, 0.2% (v/v) SDS over 30 min at 42°C. After automatic washing according to manufacturer’s instructions, the slides were hybridised for 10 h in 200 µl of ChipHybeTM buffer (Ventana Medical System, Inc). After hybridisation, the slides were washed for 2 min in 2 ×SSC/0.2% (v/v) SDS, for 2 min in 0.2 ×SSC/0.2% (v/v) SDS and for 2 min in 0.2 ×SSC, immersed briefly in isopropanol and then dried under a stream of air.

scan_protocol: The hybridization signal was detected by scanning with GenePix 4000B laser Scanner (Axon Instruments)

data_processing: The signal quantification was transformed to numerical values using the integrated GenePix software version 3.01. The raw intensities were corrected from the local background measured around each spot. First step in averaging was to calculate the mean value over spot duplicates for a given gene on the same array then quantile normalization was applied. Log-ratios of quantile normalized intensities were obtained.

organism: Saccharomyces cerevisiae

source_name: yeast culture-Ethanol non-adapted culture-60 g/l ethanol

label_protocol: Incorporation of Cyanine 3- or Cyanine 5-dCTP (Amersham Bioscience) was performed during reverse transcription of 20 µg of denaturated RNA using Label Star Reverse Transcriptase (Qiagen). Labeled cDNA was purified with MinElute spin columns (Qiagen).

extract_protocol: Extraction protocol Frozen cells (15 mg dry biomass = 19 units of OD600) were mechanically disrupted (MicroDismembrator Braun, Melsungen) and total RNA was isolated using RNeasy Mini kit (Qiagen) following the protocol of the manufacturer.

treatment_protocol: Frozen in liquid nitrogen

tag: treatment

value: Fed-Batch - Ethanol non adapted culture correspond to Fermentation II in Cot et al, (2007) FEMS Yeast Res. 7 :22-32.

tag: ethanol concentration

source_name: yeast culture-Ethanol adapted culture-60 g/l ethanol

value: Fed-Batch - Ethanol adapted culture correspond to Fermentation I in Cot et al, (2007) FEMS Yeast Res. 7 :22-32.


title: yeast-Fed-Batch-60 g/l ethanol-n°3

description: ethanol adaptation : all conditions detailed in Cot et al, (2007) FEMS Yeast Res. 7 : 22-32.


title: yeast-Fed-Batch-60 g/l ethanol-n°4


title: Cerebellum, mouse17K-A, 63 AMC170 M 495_ad-lib

status: Public on Jun 22 2009

description: 63 AMC170 M 495 A

hyb_protocol: Radiolabeled cDNA was denatured at 95 degrees C for 7 minutes and added to 12 mls of Invitrogen microhyb containing 10% dextran sulfate with Cot-1 DNA (Invitrogen) and Poly-A DNA oligos, (Sigma) added as blocking agents.  Arrays were hybridized overnight at 55 degrees C to mouse 17K-A cDNA filters.  The hybridized filters were quickly rinsed once and then washed twice at 65 degrees placed onto steel plates covered with plastic wrap and exposed to Kodak storage Phosphorimaging screens for 3-4 days.

scan_protocol: Imaging screens were scanned at 50um resolution in a Storm Phosphorimager.

data_processing: All data was extracted using ArrayPro Software and processed in Excel spreadsheets using Z normalization of each array.  Differently expressed genes were identified between the different sample groups by z-ratio analysis using an in-house microarray analysis program.

source_name: Mus musculus Cerebellum

label_protocol: ~5 ug of total RNA was radiolabeled with 33P-dCTP using Superscript II from Invitrogen.  Labeled cDNA was separated from unincorporated probe and small nucleotides using a Bio-Rad size exclusion column, Bio-Spin 30 with SSC. 1ul of each sample was counted in a scintillation counter and the remainder was used for hybridization.

extract_protocol: Qiagen RNeasy Mini Kit protocol for animal tissues after disruption using a mini-bead beater-8 and 1.0mm glass beads.

treatment_protocol: 100% regular feed, ad libitum until age of sacrifice

tag: Strain

value: C57BL/6, Tissue:Cerebellum

tag: Gender

value: male, Age:495 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 64 AMC131 F 479_ad-lib

description: 64 AMC131 F 479 A

value: female, Age:479 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 60 AMC137 F 180_ad-lib

description: 60 AMC137 F 180 A

value: female, Age:180 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 59 AMC135 M 174_ad-lib

description: 59 AMC135 M 174 A

value: male, Age:174 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 65 AMC150 F 703 C

description: 65 AMC150 F 703 C

treatment_protocol: 100% regular feed to 13 weeks of age, 90% fortified feed for 1 week, 75% fortified feed for 1 week, then 60% fortified feed until the age of sacrifice

value: female, Age:703 days Diet:Caloric restriction


title: ATM-/- IR-3

source_name: B-lymphocyte cell line GM03332 (AT, ATM -/-)

treatment_protocol: Cells were exposed to 1 Gy of IR and lysed 6 h later.

tag: genotype

value: AT, ATM -/-

tag: antibody

value: HuR

tag: vendor

value: Santa Cruz Biotech


title: Cerebellum, mouse17K-A, 61 AMC209 M 482 C

description: 61 AMC209 M 482 C

value: male, Age:482 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 55 AMC167 F 733_ad-lib

description: 55 AMC167 F 733 A

value: female, Age:733 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 66 AMC163 M 733_ad-lib

description: 66 AMC163 M 733 A

value: male, Age:733 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 58 AMC158 F 190 C

description: 58 AMC158 F 190 C

value: female, Age:190 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 57 AMC244 F 33_ad-lib

description: 57 AMC244 F 33 A

value: female, Age:33 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 56 AMC239 M 40_ad-lib

description: 56 AMC239 M 40 A

value: male, Age:40 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 62 AMC152 F 495 C

description: 62 AMC152 F 495 C

value: female, Age:495 days Diet:Caloric restriction


title: PC-2A

status: Public on Feb 26 2010

description: PDGF-C deficient mice were bred onto C57BL/6 background for more than six generations and littermates were used for all experiments.

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Mouse-6 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.

data_processing:
Data was extracted using the Illumina BeadStudio software(v1). Any spots at or below the background were filtered out using an Illumina detection p-value score of 0.02 and above. The natural log of  all remaining genes were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std.

Complete data, including detection scores, are included in the 'GSE19207_non-normalized.txt' file, which is linked to the Series GSE19207 record as a supplementary file.

source_name: Retinal (retinae) tissue, PDGF-CC treatment

extract_protocol: RNA was extracted using the TRIzol reagent (Invitrogen) followed by Qiagen RNeasy Mini kit.

treatment_protocol: After optic nerve crush (ONC), PDGF-CC protein 1 µl of active recombinant human PDGF-CC protein, 0.5 µg/µl (rhPDGF-CC) was injected into mouse vitreous once a week for two weeks. Seven days after the ONC injury and PDGF-CC protein treatment, retinae were harvested and total RNA isolated.

value: PDGF-C deficient C57BL/6

tag: gender

value: female

value: retina

value: 8 weeks

value: optic nerve crush and PDGF-CC treatment


title: yeast-Fed-Batch-60 g/l ethanol-n°2

value: Fed-Batch - Ethanol non adapted culture correspond to Fermentation II in Cot et al, (2007) FEMS Yeast Res. 7 :22-32.

value: Fed-Batch - Ethanol adapted culture correspond to Fermentation I in Cot et al, (2007) FEMS Yeast Res. 7 :22-32.


title: Cerebellum, mouse17K-A, 53 AMC56 F 714 C

description: 53 AMC56 F 714 C

value: C57BL/6, Tissue:Cerebellum

value: female, Age:714 days Diet:Caloric restriction


title: Control-2

source_name: Retinal (retinae) tissue, control

treatment_protocol: Normal retinae were harvested and total RNA isolated.

value: control


title: Cerebellum, mouse17K-A, 52 AMC130 F 481_ad-lib

description: 52 AMC130 F 481 A

value: female, Age:481 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 67 AMC174 F 704_ad-lib

description: 67 AMC174 F 704 A

value: female, Age:704 days Diet:Ad lib


title: PC-1A


title: Control-1


title: Cerebellum, mouse17K-A, 51 AMC127 M 485_ad-lib

description: 51 AMC127 M 485 A

value: male, Age:485 days Diet:Ad lib


title: PC-3


title: Control-3


title: Cerebellum, mouse17K-A, 50 AMC217 M 177 C

description: 50 AMC217 M 177 C

value: male, Age:177 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 41 AMC74 F 712_ad-lib

description: 41 AMC74 F 712 A

value: female, Age:712 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 49 AMC245 M 673 C

description: 49 AMC245 M 673 C

value: male, Age:673 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 42 AMC194 M 17_ad-lib

description: 42 AMC194 M 17 A

value: male, Age:17 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 37 AMC125 M 481_ad-lib

description: 37 AMC125 M 481 A

value: male, Age:481 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 36 AMC28 F 499 C

description: 36 AMC28 F 499 C

value: female, Age:499 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 38 AMC86 F 476_ad-lib

description: 38 AMC86 F 476 A

value: female, Age:476 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 54 AMC119 M 730_ad-lib

description: 54 AMC119 M 730 A

value: male, Age:730 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 32 AMC113 F 180 C

description: 32 AMC113 F 180 C

value: female, Age:180 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 48 AMC104 F 485 C

description: 48 AMC104 F 485 C

value: female, Age:485 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 40 AMC118 M 719_ad-lib

description: 40 AMC118 M 719 A

value: male, Age:719 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 39 AMC55 F 712 C

description: 39 AMC55 F 712 C

value: C57BL/6, Tissue:Cerebellum

value: female, Age:712 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 31 AMC31 M 194 C

description: 31 AMC31 M 194 C

value: male, Age:194 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 43 AMC241 F 40_ad-lib

description: 43 AMC241 F 40 A

value: female, Age:40 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 46 AMC92 F 169_ad-lib

description: 46 AMC92 F 169 A

value: female, Age:169 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 45 AMC133 M 180_ad-lib

description: 45 AMC133 M 180 A

value: male, Age:180 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 28 AMC73 F 714_ad-lib

description: 28 AMC73 F 714 A

value: female, Age:714 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 29 AMC193 M 19_ad-lib

description: 29 AMC193 M 19 A

value: male, Age:19 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 30 AMC198 F 21_ad-lib

description: 30 AMC198 F 21 A

value: female, Age:21 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 44 AMC115 F 174 C

description: 44 AMC115 F 174 C

value: female, Age:174 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 18 AMC34 F 194 C

description: 18 AMC34 F 194 C

value: female, Age:194 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 24 AMC48 F 499_ad-lib

description: 24 AMC48 F 499 A

value: female, Age:499 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 35 AMC101 M 485 C

description: 35 AMC101 M 485 C

value: male, Age:485 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 47 AMC148 M 495 C

description: 47 AMC148 M 495 C

value: male, Age:495 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 34 AMC53 F 194_ad-lib

description: 34 AMC53 F 194 A

value: female, Age:194 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 14 AMC72 F 716_ad-lib

description: 14 AMC72 F 716 A

value: female, Age:716 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 25 AMC208 M 673 C

description: 25 AMC208 M 673 C

value: male, Age:673 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 26 AMC25 F 743 C

description: 26 AMC25 F 743 C

value: C57BL/6, Tissue:Cerebellum

value: female, Age:743 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 20 AMC52 F 193_ad-lib

description: 20 AMC52 F 193 A

value: female, Age:193 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 33 AMC51 M 194_ad-lib

description: 33 AMC51 M 194 A

value: male, Age:194 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 22 AMC27 F 498 C

description: 22 AMC27 F 498 C

value: female, Age:498 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 15 AMC186 M 44_ad-lib

description: 15 AMC186 M 44 A

value: male, Age:44 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 19 AMC50 M 193_ad-lib

description: 19 AMC50 M 193 A

value: male, Age:193 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 13 AMC36 M 743_ad-lib

description: 13 AMC36 M 743 A

value: male, Age:743 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 17 AMC30 M 193 C

description: 17 AMC30 M 193 C

value: male, Age:193 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 16 AMC197 F 19_ad-lib

description: 16 AMC197 F 19 A

value: female, Age:19 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 08 AMC4 F 491 C

description: 08 AMC4 F 491 C

value: female, Age:491 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 09 AMC43 M 498_ad-lib

description: 09 AMC43 M 498 A

value: male, Age:498 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 10 AMC46 F 498_ad-lib

description: 10 AMC46 F 498 A

value: female, Age:498 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 04 AMC33 F 193 C

description: 04 AMC33 F 193 C

value: female, Age:193 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 03 AMC7 M 186 C

description: 03 AMC7 M 186 C

value: male, Age:186 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 23 AMC80 M 476_ad-lib

description: 23 AMC80 M 476 A

value: male, Age:476 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 01 AMC185 M 43_ad-lib

description: 01 AMC185 M 43 A

value: male, Age:43 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 02 AMC196 F 17_ad-lib

description: 02 AMC196 F 17 A

value: C57BL/6, Tissue:Cerebellum

value: female, Age:17 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 07 AMC57 M 474 C

description: 07 AMC57 M 474 C

value: male, Age:474 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 06 AMC23 F 186_ad-lib

description: 06 AMC23 F 186 A

value: female, Age:186 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 05 AMC21 M 186_ad-lib

description: 05 AMC21 M 186 A

value: male, Age:186 days Diet:Ad lib


title: Cerebellum, mouse17K-A, 21 AMC58 M 472 C

description: 21 AMC58 M 472 C

value: male, Age:472 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 11 AMC207 M 673 C

description: 11 AMC207 M 673 C

value: male, Age:673 days Diet:Caloric restriction


title: Cerebellum, mouse17K-A, 12 AMC1 F 736 C

description: 12 AMC1 F 736 C

value: female, Age:736 days Diet:Caloric restriction


title: Thymocytes 16month #1 Cy-3

status: Public on May 05 2009

description:
Isolated thymocytes from a 16 month old C57BL/6 mouse
Test channel of GSM400012

hyb_protocol: 750 ng of Cy3-labeled cRNA and 750 ng of Cy5-labeled control sample were combined with spiked in control probes specific for targets on the arrays and hybridized over night at 600C to Agilent Mouse Whole Genome 44K Oligo Microarrays (Agilent Technologies, Palo Alto, CA). The arrays were washed at room temperature 6X SSC with 0.005% Triton X-102 for 10 minutes and 0.01x SSC with 0.005% Triton X-102 at 4 degrees C for 5 minutes. The slides were then dried in a nitrogen stream.

scan_protocol: Arrays were scanned at a 10um resolution using an Agilent Microarray Scanner, G2565AA .

data_processing: Data from both the Cy-3 and the Cy5 channels was extracted using the Agilent Feature Extraction Software, Version 7.1.  Results for control probes were first removed, multiple repeats of any probe were averaged, then each array was z-normalized. In short, the natural log of the remaining genes were used to find the avg and std of each array and the z-score normalization was calculated:  Z-score = (raw value - avg)/std.  Results for the Cy-3 and Cy-5 channels will be reported separately.  In order to be selected for the final gene list, the expression value of a particular gene had to be at least 1.5 times different from the Z score of the control. Differences were considered statistically significant only if they had a p value less than 0.01.  Complete data on all spots will be included in the supplemental files.

source_name: Thymocytes 16month #1

label_protocol: total RNA was used to generate fluorescent cRNA for use with Agilent’s oligonucleotide microarrays. The RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit following manufactures protocols. In Short: Between 0.5ug to 2ug of total RNA was used to generate first and second strands of cDNA containing a T7 RNA polymerase promoter. Then cRNA was synthesized using T7 RNA polymerase which simultaneously incorporates cyanine 3- or cyanine 5- labeled CTP (Perkin Elmer, Wellesley, MA). Qiagen RNeasy columns (Qiagen Valencia, CA) were used to purify the labeled cRNA and the final concentration was assessed using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies,

extract_protocol: For each array sample, the RNA was prepared from purified thymocytes. The thymocytes were processed by using the RNeasy Mini Kit (Qiagen, Valencia, CA). Quality and quantity of the  total RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Freshly-extracted thymi from mice of various ages were dissociated in RPMI using a syringe and forceps. Cell clumps were broken up with repeated pipetting and then poured through 70um nylon mesh cell strainers (BD Falcon, Bedford, MA) to remove connective tissue and any remaining clumps. The cells were washed once to remove fat cells and red blood cells were lysed with ammonium chloride buffer. The remaining thymocyte population was counted, washed twice in RPMI followed by PBS.

value: Isolated thymocytes

value: 16 month old

value: C57BL/6 mouse


title: Thymocytes 24month #2 Cy-3

description:
Isolated thymocytes from a 24 month old C57BL/6 mouse
Test channel of GSM400016

source_name: Thymocytes 24month #2

value: 24 month old


title: Thymocytes 1month #9 Cy-5

description:
Isolated thymocytes from a 1 month old C57BL/6 mouse
Reference channel of GSM400026

source_name: Thymocytes 1month #9

value: 1 month old


title: Thymocytes 1month #8 Cy-5

description:
Isolated thymocytes from a 1 month old C57BL/6 mouse
Reference channel of GSM400025

source_name: Thymocytes 1month #8


title: Thymocytes 6month #1 Cy-3

description:
Isolated thymocytes from a 6 month old C57BL/6 mouse
Test channel of GSM400009

source_name: Thymocytes 6month #1

value: 6 month old


title: Thymocytes 16month #3 Cy-3

description:
Isolated thymocytes from a 16 month old C57BL/6 mouse
Test channel of GSM400014

source_name: Thymocytes 16month #3


title: Thymocytes 6month #2 Cy-3

description:
Isolated thymocytes from a 6 month old C57BL/6 mouse
Test channel of GSM400010

source_name: Thymocytes 6month #2


title: Thymocytes 1month #5 Cy-5

description:
Isolated thymocytes from a 1 month old C57BL/6 mouse
Reference channel of GSM400022

source_name: Thymocytes 1month #5


title: Thymocytes 6month #3 Cy-3

description:
Isolated thymocytes from a 6 month old C57BL/6 mouse
Test channel of GSM400011

source_name: Thymocytes 6month #3


title: Thymocytes 1month #6 Cy-5

description:
Isolated thymocytes from a 1 month old C57BL/6 mouse
Reference channel of GSM400023

source_name: Thymocytes 1month #6


title: Thymocytes 24month #1 Cy-3

description:
Isolated thymocytes from a 24 month old C57BL/6 mouse
Test channel of GSM400015

source_name: Thymocytes 24month #1


title: Thymocytes 16month #2 Cy-3

description:
Isolated thymocytes from a 16 month old C57BL/6 mouse
Test channel of GSM400013

source_name: Thymocytes 16month #2


title: Thymocytes 1month #7 Cy-5

description:
Isolated thymocytes from a 1 month old C57BL/6 mouse
Reference channel of GSM400024

source_name: Thymocytes 1month #7


title: Thymocytes 24month #3 Cy-3

description:
Isolated thymocytes from a 24 month old C57BL/6 mouse
Test channel of GSM400017

source_name: Thymocytes 24month #3


title: Thymocytes 1month #4 Cy-5

description:
Isolated thymocytes from a 1 month old C57BL/6 mouse
Reference channel of GSM400021

source_name: Thymocytes 1month #4


title: Thymocytes 1month #2 Cy-5

description:
Isolated thymocytes from a 1 month old C57BL/6 mouse
Reference channel of GSM400019

source_name: Thymocytes 1month #2


title: Thymocytes 1month #3 Cy-5

description:
Isolated thymocytes from a 1 month old C57BL/6 mouse
Reference channel of GSM400020

source_name: Thymocytes 1month #3


title: Donor #3 CCL19-Migrated, T cells From Donor 3, no treatment

status: Public on Jan 01 2009

description: Donor #3 CCL19-Migrated

hyb_protocol: Cy3 and Cy5 probes were applied to the Human 44K whole genome oligo array kit. Slides were hybridized in a rotating chamber overnight at 60°C, and washed on next day in 6X SSC, 0.005% Triton X-102 for 10 minutes, and then in 0.1X SSC, 0.005% Triton X-102 for 5 minutes on ice. Slides were dried using a nitrogen-filled air gun, and scanned with an Agilent scanner.

scan_protocol: Arrays were scanned at a 10um resolution using an Agilent Scanner G2565AA .

data_processing: Data from both the Cy-3 and the Cy5 channels was extracted using the Agilent Feature Extractor Software, Version 7.5.  Results for control probes were first removed, multiple repeats of any probe were averaged, then each array was z-normalized. In short, the natural log of the remaining genes were used to find the avg and std of each array and the z-score normalization was calculated:  Z-score = (raw value - avg)/std.  Complete data on all spots will be included in the supplemental files.

source_name: T cells From Donor 3, no treatment

label_protocol: cDNA was made from total mRNA using the BIO-RAD (Hercules, CA) cDNA synthesis kit. Then cRNA was made from cDNA, amplified and labeled with Cy-5 using the Agilent low-input linear amplification kit, according to manufacturer’s protocols.

extract_protocol: Total RNA was isolated by  Trizol (Invitrogen, Carlsbad, CA), method using the RNA isolation kit (Quigen, Valencia, CA). RNA quality and quantity were analyzed using the Agilent Bioanlayzer platform (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Blood was collected from healthy human donors, PBMCs were isolated from blood using Ficoll gradients and T cells were purified using R&D Systems T cell enrichment columns. T cells were put in six-well plates and were cultured in media alone.  Number of cells were always kept equal in terms of chemokines. All of the chambers and plates were incubated for 3 h in a humidified incubator at 37°C with 5% CO2. After incubation, the cells were harvested from the plates for RNA isolation.

tag: T cells from a healthy  donor


title: N0

status: Public on Mar 07 2009

description: Naïve CD8 T cells from a pool of healthy donors

hyb_protocol: 3 unique biological replicates of each cell type and treatment protocol were hybed to human 4X44K arrays.  In short, 825ng of each of the Cy3 sample probes and Cy5 control probe were combined with 10X Blocking Agent, 25X Fragmentation Buffer and nuclease free water to 55ul and then denatured at 60°C for 30 minutes. Samples were then mixed with 55ul of Hi-RPM hybridization buffer and applied to the Human 4X44K whole genome oligo arrays using Sure-Hyb chambers and hybridized for 17 hours in a rotating chamber at 65°C. Slides were washed the following day using the Agilent wash buffers, twice at room temperature in buffer#1 and once at ~31°C in buffer #2, then dried using a stream of nitrogen and scanned.

scan_protocol: Arrays were scanned at a 5um resolution using the extended dynamic range protocol on an upgraded Agilent microarray scanner, model G2565AA.

data_processing: Data from both the Cy-3 and the Cy5 channels was extracted using the Agilent Feature Extractor Software, Version 7.5.  The normalization consisted of a log10 transformation of both channels and the Cy-3 channels were normalized to the intensity of the Cy-5 control channel ( log10cy3 - log10cy5) + mean log10cy5 signals.  The results from 3 biological replicates were then averaged to give the VALUE below.

label_protocol: Total RNA (500 ng) was reverse transcribed to make double stranded cDNA using a T7 containing oligo-dT primer and the Agilent low RNA Input Linear Amplification Kit.  This was followed by cRNA synthesis with T7 RNA polymerase in the presence of 0.3 mM cyanine 3-CTP (Cy3), from the same kit.  The labeled probes were cleaned up and concentrated with Qiagen's RNeasy mini spin columns. The quantity of amplified cRNA was measured by a NanoDrop small volume spectrophotometer.

extract_protocol: Total RNA was extracted from freshly isolated (0Hr) and stimulated (16 hours) naïve, TCM and TEM CD8 T cells (by STAT60) from 12 different healthy adult donors to form 4 RNA pools.  The quality and quantity of total RNA were analyzed by an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).  Three pools of RNA were used in the microarray experiment.

treatment_protocol: Sorted naïve, TCM, and TEM CD8 T cells were either used right away or incubated with anti-CD3 and anti-CD28 Ab (anti-CD3/CD28) coupled magnetic beads (Invitrogen) at the cell:bead ratio of 1:1 for 16 hours in RPMI-1640 with 10% Fetal bovine serum and penicillin (10 U/ml)/streptomycin (10 ug/ml) (Invitrogen).  The freshly isolated and 16 hr stimulated cells from several donors as a pool were used for gene expression microarray analysis.

tag: Blood was collected from healthy human donors, PBMCs were isolated from blood using Ficoll gradients. Naive and memory CD8 T cells were then enriched by removing other types of cells through incubation with a panel of mouse mAbs against CD4, CD19, CD11b, CD14, CD16, MHC class II, erythrocytes, platelets, and CD45RO (for the enrichment of naïve cells) or CD45RA (for that of memory cells). Ab-bound cells were subsequently removed by incubation with anti-mouse IgG-conjugated magnetic beads (Qiagen, Valencia, CA).  These enriched naïve and memory CD8 T cells were further purified into CD8+CD45RA+CD62L+ naïve T cells, CD8+CD45RA-CD62L+ central memory T cells (TCM), and CD8+CD45RA-CD62L- effector memory T cells (TEM) by a cell sorter (MoFlo; Dako Cytomation, Carpentaria, CA).

source_name: Stratagene’s Universal Human Reference RNA (Stratagene, La Jolla, CA).

label_protocol: Total RNA (1200 ng) was reverse transcribed to make double stranded cDNA using a T7 containing oligo-dT primer and the Agilent low RNA Input Linear Amplification Kit.  This was followed by cRNA synthesis with T7 RNA polymerase in the presence of 0.3 mM cyanine 5-CTP (Cy5), from the same kit. The labeled probe was cleaned up and concentrated with Qiagen's RNeasy mini spin columns. The quantity of amplified cRNA was measured by a NanoDrop small volume spectrophotometer.

extract_protocol: Unknown

treatment_protocol: Equal quantities of DNase-treated total RNA from each of the 10 cell lines were pooled to make the Universal Human Reference RNA.

tag: Stratagene’s Universal Human Reference RNA is composed of total RNA from 10 human cell lines.


title: EMS

description: Effector memory T cells (TEM) stimulated by incubation with anti-CD3 and anti-CD28 Ab.

hyb_protocol: 3 unique biological replicates of each cell type and treatment protocol were hybed to human 4X44K arrays.  In short, 825ng of each of the Cy3 sample probes and Cy5 control probes were combined with 10X Blocking Agent, 25X Fragmentation Buffer and nuclease free water to 55ul and then denatured at 60°C for 30 minutes. Samples were then mixed with 55ul of Hi-RPM hybridization buffer and applied to the Human 4X44K whole genome oligo arrays using Sure-Hyb chambers and hybridized for 17 hours in a rotating chamber at 65°C. Slides were washed the following day using the Agilent wash buffers, twice at room temperature in buffer#1 and once at ~31°C in buffer #2, then dried using a stream of nitrogen and scanned.

label_protocol: Total RNA (500 ng) was reverse transcribed to make double stranded cDNA using a T7 containing oligo-dT primer and tnullhe Agilent low RNA Input Linear Amplification Kit.  This was followed by cRNA synthesis with T7 RNA polymerase in the presence of 0.3 mM cyanine 3-CTP (Cy3), from the same kit.  The labeled probes were cleaned up and concentrated with Qiagen's RNeasy mini spin columns. The quantity of amplified cRNA was measured by a NanoDrop small volume spectrophotometer.


title: Donor #3 CCL19-Migrated, T cells from donor 3 that migrated towards CCL21

description: Donor #3 CCL19-Migrated

label_protocol: cDNA was made from total mRNA using the BIO-RAD (Hercules, CA) cDNA synthesis kit. Then cRNA was made from cDNA, amplified and labeled with Cy-3 using the Agilent low-input linear amplification kit, according to manufacturer’s protocols.

treatment_protocol: Blood was collected from healthy human donors, PBMCs were isolated from blood using Ficoll gradients and T cells were purified using R&D Systems T cell enrichment columns. T cells were put in six-well plates and treated with 100 ng/ml of CXCL12.  Number of cells were always kept equal in terms of chemokines. All of the chambers and plates were incubated for 3 h in a humidified incubator at 37°C with 5% CO2. After incubation, the cells were harvested from the plates for RNA isolation.

tag: T cells from a healthy donor


title: NS

description: Naïve CD8 T cells from a pool of healthy donors stimulated for 16 hours with anti-CD3 and anti-CD28 Antibody.


title: Donor #3 CXCL12-Migrated, T cells from donor 3 that migrated towards CXCL14

description: Donor #3 CXCL12-Migrated


title: CM0

description: Central memory T cells (TCM)

source_name: Central memory T cells (TCM)


title: CMS

description: Central memory T cells (TCM) stimulated by incubation with anti-CD3 and anti-CD28 Ab.


title: EM0

description: Effector memory T cells (TEM)

source_name: Effector memory T cells (TEM)


title: Donor #3 CXCL12-Migrated, T cells From Donor 3, no treatment

description: Donor #3 CXCL12-Migrated


title: Donor #3 CCL19, T cells From Donor 3, no treatment

description: Donor #3 CCL19


title: Donor #3 CXCL12, T cells From Donor 3, CXCL12 Treatment

description: Donor #3 CXCL12

source_name: T cells From Donor 3, CXCL12 Treatment


title: Donor #3 CXCL12, T cells From Donor 3, no treatment

description: Donor #3 CXCL12


title: Donor #3 CCL19, T cells from donor 3, CCL19 Treatment

description: Donor #3 CCL19

source_name: T cells from donor 3, CCL19 Treatment


title: Donor #2 CXCL12-Migrated, T cells From Donor 2, no treatment

description: Donor #2 CXCL12-Migrated

source_name: T cells From Donor 2, no treatment


title: Donor #2 CXCL12-Migrated, T cells from donor 2 that migrated towards CXCL13

description: Donor #2 CXCL12-Migrated


title: Donor #1 CXCL12-Migrated, T cells from donor 1 that migrated towards CXCL12

description: Donor #1 CXCL12-Migrated


title: Donor #2 CXCL12, T cells From Donor 2, no treatment

description: Donor #2 CXCL12


title: Donor #2 CCL19-Migrated, T cells from donor 2 that migrated towards CCL20

description: Donor #2 CCL19-Migrated


title: Donor #2 CCL19, T cells from donor 2, CCL19 Treatment

description: Donor #2 CCL19

source_name: T cells from donor 2, CCL19 Treatment


title: Donor #2 CCL19, T cells From Donor 2, no treatment

description: Donor #2 CCL19


title: BG-1 pre-mir-200c 2

status: Public on Aug 29 2008

description: Microarray expression data generated from Illumina Human_Ref-8_V2 Sentrix BeadChips hybridized and scanned using a single channel of Cy3 fluorescent label.

hyb_protocol: A total of 0.85ug of biotin-labeled cRNA was hybridized for 16 hours to Illumina's Sentrix MouseRef-8 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts per sample with approximately 30-fold redundancy. The arrays were washed at both 55 degrees C and room temperature and then blocked. The biotinylated cRNA was detected with streptavidin-Cy3, washed a final time and the arrays were dried by spinning at 500 RPM for 4 minutes.

scan_protocol: Slides were scanned using Illumina's BeadStation 500X Genetic Analysis Systems scanner. The image data was extracted using BeadStudio software, version 3. (Illumina)

data_processing: Raw microarray data was analyzed using DIANE 6.0, a spreadsheet-based microarray analysis program.  Microarray intensities were subjected to Z normalization.  i.e. [(intensity of sample #1 from array A - avarage of all intensities from array A)/ standard diviation of all of intensities on array A].  Differently expressed cRNA species were identified between the different sample groups by  the ratio of these normalized intensities.

source_name: Ovary

label_protocol:
Streptavidin-Cy3 bound to cRNA amplified with biotin-16-UTP using the Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791).
A 0.5ug aliquot of total RNA from each sample was labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791). RNA was first converted into single-stranded cDNA using reverse transcription and an oligo-dT primer containing the T7 RNA polymerase promoter then the single-stranded cDNA was copied to produce double-stranded cDNA molecules. The double-stranded cDNA was used in an overnight in vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP.

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: Transfected with precursor miRNA hsa-miR-200c (Ambion) using siPORT NeoFX (Ambion)

tag: poorly differentiated papillary carcinoma

value: female


title: Donor #1 CCL19-Migrated, T cells from donor 1 that migrated towards CCL19

description: Donor #1 CCL19-Migrated


title: Donor #1 CCL19, T cells From Donor 1, no Treatment

description: Donor #1 CCL19

source_name: T cells From Donor 1, no Treatment


title: UCI101 pre-let-7a2

treatment_protocol: Transfected with precursor miRNA hsa-let-7a (Ambion) using siPORT NeoFX (Ambion)

tag: Papillary ovarian carcinoma


title: BG-1 pre-let-7f 2

treatment_protocol: Transfected with precursor miRNA hsa-let-7f (Ambion) using siPORT NeoFX (Ambion)


title: UCI101 pre-mir-424 2

treatment_protocol: Transfected with precursor miRNA hsa-miR-424 (Ambion) using siPORT NeoFX (Ambion)


title: BG-1 pre-mir-34c 2

treatment_protocol: Transfected with precursor miRNA hsa-miR-34c (Ambion) using siPORT NeoFX (Ambion)


title: BG-1 siC 2

treatment_protocol: Transfected with control siRNA #1 (Dharmacon) using siPORT NeoFX (Ambion)


title: Donor #1 CXCL12, T cells From Donor 1, no Treatment

description: Donor #1 CXCL12


title: Donor #1 CXCL12, T cells From Donor 1, CXCL12 Treatment

description: Donor #1 CXCL12

source_name: T cells From Donor 1, CXCL12 Treatment


title: Donor #2 CXCL12, T cells From Donor 2, CXCL12 Treatment

description: Donor #2 CXCL12

source_name: T cells From Donor 2, CXCL12 Treatment


title: Donor #2 CCL19-Migrated, T cells From Donor 2, no treatment

description: Donor #2 CCL19-Migrated


title: BG-1 pre-mir-424 2


title: Donor #1 CCL19-Migrated, T cells From Donor 1, no Treatment

description: Donor #1 CCL19-Migrated


title: Donor #1 CXCL12-Migrated, T cells From Donor 1, no Treatment

description: Donor #1 CXCL12-Migrated


title: UCI101 pre-let-7f 2


title: BG-1 pre-mir-98 2

treatment_protocol: Transfected with precursor miRNA hsa-miR-98 (Ambion) using siPORT NeoFX (Ambion)


title: Donor #1 CCL19, T cells from donor 1, CCL19 Treatment

description: Donor #1 CCL19

source_name: T cells from donor 1, CCL19 Treatment


title: UCI101 pre-mir-34c 2


title: UCI101 pre-mir-98 2


title: UCI101 siC 2


title: BG-1 pre-let-7f 1


title: BG-1 pre-mir-424 1


title: BG-1 pre-mir-34c 1


title: UCI101 pre-let-7f 1


title: BG-1 pre-mir-200c 1


title: UCI101 pre-let-7a1


title: BG-1 siC 1


title: UCI101 pre-mir-424 1


title: UCI101 pre-mir-98 1