title: female,NZW/LacJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: wildtype

value: NZW/LacJ

value: female

value: 2 months


title: female,CBA/J,strain, dorsal root ganglion tissue

status: Public on Feb 18 2015

type: RNA

city: San Diego

first: John

last: Walker

state: CA

address: 10675 John Jay Hopkins Dr

country: USA

institute: NIBR

description: Gene expression data from wildtype mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse MOE_430_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: CEL files were processed using GCRMA in R (version 2.6.2 (2008-02-08)), using packages downloaded from Bioconductor

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: cDNA and amplified antisense RNA was made from 1.4 mg of pooled total RNA, using the Affymetrix Single Amplification protocol.

growth_protocol: DRGs were dissected from naïve 2-month-old mice of both sexes (n=3 mice/sex/strain) between 09:00–12:00 h

extract_protocol: Total RNA was isolated from tissues using Trizol (Invitrogen) followed by RNeasy (Qiagen, Valencia, CA).

treatment_protocol: wildtype mice

tag: tissue

value: dorsal root ganglion

tag: genotype

tag: strain

value: CBA/J

tag: gender

tag: age


title: female,c57BL/6J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: female,DBA/2J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: male,A/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: A/J

value: male


title: male,DBA/2J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: female,BTBT T+tf/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: BTBT T+tf/J


title: female,BALB/CByJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: BALB/CByJ


title: female,AKR/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: AKR/J


title: male,MRL/MpJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: MRL/MpJ


title: female,129S1/Sv1mJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: male,SWR/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: SWR/J


title: male,C57BR/cdJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: male,PL/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: PL/J


title: male,C58/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: male,BUB/BnJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: BUB/BnJ


title: male,C3H/HeJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice


title: male,NON/LtJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: NON/LtJ


title: male,FVB/NJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: FVB/NJ


title: male,NOD/LtJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: wildtype

value: NOD/LtJ


title: male,P/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: P/J


title: male,RIIIS/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: RIIIS/J

value: 2 months


title: male,KK/HIJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: dorsal root ganglion

value: KK/HIJ


title: male,SM/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: SM/J

value: male


title: male,NZO/HILtJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: NZO/HILtJ


title: male,CBA/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: CBA/J


title: male,NZW/LacJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: NZW/LacJ


title: HfQ3-cy5_WT3-cy3

status: Public on Jul 15 2014

city: Paris

first: Marc

last: Monot

address: 28 rue du docteur roux

country: France

institute: Institut Pasteur

description: Biological replicate 3 of 4.

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers.

scan_protocol: Scanned on a GenePix Pro 6 dual-channel laser scanner.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicate : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridioides difficile

source_name: hfQ mutant grown 7.5h Tyt

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with Cy5 or Cy3 dyes 1h at room temperature in the dark.

growth_protocol: C. difficile strain C630E and hfQ mutant were grown in Tyt.

extract_protocol: Total RNA was extracted using QIAgen RNeasy kit.

tag: strain/background

value: C630E Mullany hfQ::erm

tag: genotype/variation

value: hfQ mutation

source_name: 630E strain grown 7.5h in Tyt (reference)

value: C630E Mullany

value: wild-type


title: male,AKR/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: AKR/J


title: HfQ2-cy3_WT2-cy5

description: Biological replicate 2 of 4.


title: DU145 xenograft in NOD/SCID mice_vehicle_4 weeks

status: Public on Jan 23 2015

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on HG_U133_2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Affymetrix GeneChip Expression Manual 701021 Rev.5)

growth_protocol: DU145 xenograft tumors were established by using early-passage cells and maintained in NOD.CB17-Prkdc(SCID) mice. For s.c. tumor development, 100 μL of collagen-embedded cells was injected s.c. into 5- to 8-week-old NOD.CB17-Prkdc(SCID) mice. The mice were observed for 3–5 months for appearance and development of tumors.

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

tag: cell type

value: DU145 xenograft in NOD/SCID mice

tag: dose

value: 0 mg/kg, intravenous

tag: schedule

value: once per week


title: male,SJL/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: wildtype

value: SJL/J


title: HfQ4-cy5_WT4-cy3

description: Biological replicate 4 of 4.


title: rpoS_rep1

status: Public on May 05 2014

type: SRA

description:
Processed data file: GSE46380_S_Norel_statistics_WT-rpoSdb.xls
Processed data file: GSE46380_S_Norel_statistics_rpoSdb-deltarpoS.xls

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and for low-quality sequence using in-house program. Only sequence with a minimum length of 30 were considered, then mapped to 14028S whole genome sequence and plasmid (CP001363.1 and CP001362.1) using bowtie v0.12.7 with parameters --chunkmbs 200 -m 50 -e 59 -a --best --solexa1.3-quals
HTseq-count was used for counting genes with parameters -m -intersection-nonempty -s yes -t gene
Statistical analyses were performed using R version 2.15.1 and Bioconductor packages. Genes with nul raw counts in the nine samples were excluded from the data table. Normalisation and differential analysis were performed using DESeq version 1.8.3.
The whole dataset was first normalized using the normalization function of DESeq and dispersion was estimated with default parameters.
The statistical test was then applied on pairs of strains. Resulting p-values were adjusted for multiple comparisons according to the BH method. Two significance thresholds (0.05 and 0.001) were applied on adjusted p-values in order to declare genes as differentially expressed.
Genome_build: GenBank CP001363.1 and CP001362.1 (14028S).
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name, Salmonella typhimurium LT2 orthologs), Raw Counts (WT, Delta-rpoS, rpoSdb), Normalized Counts (WT, Delta-rpoS, rpoSdb), Statistics (rpoSdb/WT, Delta-rpoS/WT, Delta-rpoS/rpoSdb).

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Mutant rpoS double mutation 14028S

growth_protocol: Strains were grown aerobically to late stationary phase in rich medium (LB, 37°C, 200 rpm, 18h).

extract_protocol:
Total RNA was isolated from Salmonella cells using TRIzol, digested with DNase I and the RNA quality was analyzed using an Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: rpoS double mutation


title: male,BTBT T+tf/J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: dorsal root ganglion

value: BTBT T+tf/J

value: 2 months


title: male,129S1/Sv1mJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: male


title: DU145 xenograft in NOD/SCID mice_NVP-BEZ235 and taxotere_4 weeks

value: 10 mg/kg, intravenous for taxotere, 12.5 mg/kg perorally for NVP_BEZ235

value: once per week for taxotere and once per day for NVP_BEZ235


title: HfQ1-cy3_WT1-cy5

description: Biological replicate 1 of 4.

value: C630E Mullany hfQ::erm


title: male,BALB/CByJ,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: BALB/CByJ


title: Conventional_purified_diet

status: Public on Jan 08 2015

hyb_protocol: Standard Affymetrix protocols

scan_protocol: standard Affymetrix procedures

data_processing: gcRMA, unlogged using R

label_protocol: GeneChip 3' IVT Express kits (Affymetrix) were used to amplify cRNA from 500 ng total RNA.

extract_protocol: An approximately 5 mm2 section of frozen liver tissue was placed in a 2.0 ml tube with a steel bead and 1ml Trizol reagent (Invitrogen).  Following disruption in a Qiagen Tissuelyser 200ul of chloroform was added to the homogenate, mixed and centrifuged.  The aqueous layer containing the RNA was transferred to a tube containing 500ul of ice cold isopropanol and mixed.  This mixture was loaded onto an RNeasy spin column (Qiagen) and RNA was washed and eluted as per manufacturer’s instructions.  For microarray analysis, the integrity and concentration of RNA was determined on an Experion instrument (BioRad). Samples were pooled based on experimental condition.

treatment_protocol: Conventional and germ free mice were maintained on purified diet, cholic acid diet or deoxycholic acid diet for two weeks.  After being fasted overnight animals were anesthetized with isoflurane and liver and bile samples were collected and snap frozen for further analysis.

value: Swiss Webster

value: Conventional

tag: diet


title: rpoS_rep0


title: rpoS_rep2


title: Hfq3-cy3_WT3-cy5

description: Biological replicate 3 of 4.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

source_name: Hfq antisense grown 7.5h Tyt

growth_protocol: C. difficile strain C630E and Hfq antisense strains were grown in Tyt.

value: C630E Mullany Hfq antisense

value: Hfq antisense

value: C630E Mullany

value: wild-type


title: Hfq4-cy5_WT4-cy3

description: Biological replicate 4 of 4.


title: Hfq2-cy5_WT2-cy3

description: Biological replicate 2 of 4.


title: Germ-free_cholic_acid_diet

value: Germ-free


title: Delta_rep2

description:
Processed data file: GSE46380_S_Norel_statistics_WT-deltarpoS.xls
Processed data file: GSE46380_S_Norel_statistics_rpoSdb-deltarpoS.xls

source_name: Mutant rpoS 14028S

value: delta-rpoS


title: Conventional_cholic_acid_diet


title: DU145 xenograft in NOD/SCID mice_taxotere_4 weeks

value: DU145 xenograft in NOD/SCID mice

value: 10 mg/kg, intravenous

value: once per week


title: WT_rep2

description:
Processed data file: GSE46380_S_Norel_statistics_WT-rpoSdb.xls
Processed data file: GSE46380_S_Norel_statistics_WT-deltarpoS.xls

source_name: Wild-type strain 14028S

value: wild type


title: Delta_rep0


title: Delta_rep1


title: Hfq1-cy3_WT1-cy5

description: Biological replicate 1 of 4.


title: Germ-free_DCA_diet


title: Germ-free_purified_diet


title: DU145 xenograft in NOD/SCID mice_NVP-BEZ235_4 weeks

value: 12.5 mg/kg, perorally

value: once per day


title: WT_rep0


title: WT_rep1


title: Conventional_DCA_diet


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-tu3

status: Public on Mar 14 2014

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Alk; Sample name: 6-tu3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
JMP Genomics
Background correction: RMA; Transformation: log2; Normalization: median scaling; Summary method: median

label: Biotin

source_name: CD8 T cells isolated from tumor

label_protocol: One cycle amplification by standard Affymetrix procedure

extract_protocol: Trizol, per manufacturers protocol

value: CD8 T cells

tag: transduction

value: shRNA targeting Alk

value: tumor

tag: sample name


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-tu1

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Arhgap5; Sample name: 5-tu1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

value: shRNA targeting Arhgap5


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-tu2

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Alk; Sample name: 6-tu2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: male,c57BL/6J,strain, dorsal root ganglion tissue

description: Gene expression data from wildtype mice

value: dorsal root ganglion

value: wildtype

value: male

value: 2 months


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-tu3

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Ptpn2; Sample name: 4-tu3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

value: shRNA targeting Ptpn2


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-tu1

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Ptpn2; Sample name: 4-tu1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-tu1

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Alk; Sample name: 6-tu1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-tu3

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Arhgap5; Sample name: 5-tu3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-tu3

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Egr2; Sample name: 3-tu3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

value: shRNA targeting Egr2


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-tu2

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Egr2; Sample name: 3-tu2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-tu2

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Ptpn2; Sample name: 4-tu2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-tu1

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Lacz; Sample name: 1-tu1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

value: shRNA targeting Lacz


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-sp3

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Alk; Sample name: 6-sp3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

source_name: CD8 T cells isolated from spleen

value: spleen


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-sp2

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Arhgap5; Sample name: 5-sp2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-tu2

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Lacz; Sample name: 1-tu2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-tu2

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-tu2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

value: shRNA targeting Ppp2r2d


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-sp3

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Arhgap5; Sample name: 5-sp3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-sp2

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Ptpn2; Sample name: 4-sp2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-tu1

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-tu1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-tu1

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Egr2; Sample name: 3-tu1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-sp3

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Ptpn2; Sample name: 4-sp3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-tu3

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Lacz; Sample name: 1-tu3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-tu3

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-tu3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-sp1

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Arhgap5; Sample name: 5-sp1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-sp2

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Alk; Sample name: 6-sp2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-tu2

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Arhgap5; Sample name: 5-tu2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-sp1

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Alk; Sample name: 6-sp1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-sp3

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Egr2; Sample name: 3-sp3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-sp1

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-sp1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: CD630_WT2-cy5_spoIIID2-cy3

status: Public on Feb 20 2014

description: Biological replicate 2 of 2.

source_name: strain C630E grown 15h in MS (reference)

growth_protocol: C. difficile strain C630E was grown for 15 hours in MS medium.

extract_protocol: Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.

value: C630E Mullany

value: wild-type

source_name: spoIIID mutant grown 15h in MS

value: spoIIID mutant


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-sp3

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-sp3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-sp1

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Lacz; Sample name: 1-sp1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-sp2

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-sp2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-sp2

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Egr2; Sample name: 3-sp2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: CD630_WT1-Cy3_sigK1-Cy5

description: Biological replicate 1 of 4.

source_name: strain C630E grown 24h in MS (reference)

growth_protocol: C. difficile strain C630E was grown for 24 hours in MS medium.

tag: growth condition

value: MS medium

source_name: sigK mutant grown 24h in MS

value: sigK mutation


title: CD630_WT3-Cy3_sigF3-Cy5

description: Biological replicate 3 of 4.

source_name: strain C630E grown 14h in MS (reference)

growth_protocol: C. difficile strain C630E was grown for 14 hours in MS medium.

source_name: sigF mutant grown 14h in MS

value: sigF mutation


title: CD630_WT3-Cy3_sigG3-Cy5

description: Biological replicate 3 of 4.

source_name: strain C630E grown 19h in MS (reference)

growth_protocol: C. difficile strain C630E was grown for 19 hours in MS medium.

source_name: sigG mutant grown 19h in MS

value: sigG mutation


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-sp1

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Egr2; Sample name: 3-sp1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

value: CD8 T cells


title: CD630_WT4-Cy5_sigG4-Cy3

description: Biological replicate 4 of 4.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-sp3

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Lacz; Sample name: 1-sp3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: CD630_WT3-Cy5_sigK3-Cy3

description: Biological replicate 3 of 4.


title: CD630_WT2-Cy5_sigG2-Cy3

description: Biological replicate 2 of 4.


title: CD630_WT4-Cy3_sigF4-Cy5

description: Biological replicate 4 of 4.


title: CD630_WT1-Cy3_sigG1-Cy5

description: Biological replicate 1 of 4.


title: CD630_WT2-Cy5_sigF2-Cy3

description: Biological replicate 2 of 4.


title: CD630_WT1-cy3_SpoIIID1-cy5

description: Biological replicate 1 of 2.


title: CD630_WT2-Cy3_sigK2-Cy5

description: Biological replicate 2 of 4.


title: CD630_WT4-Cy5_sigK4-Cy3

description: Biological replicate 4 of 4.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-sp1

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Ptpn2; Sample name: 4-sp1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-sp2

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Lacz; Sample name: 1-sp2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: CD630_WT4-Cy3_sigE4-Cy5

description: Biological replicate 4 of 4.

source_name: sigE mutant grown 14h in MS

value: sigE mutation


title: CD630_WT3-Cy3_sigE3-Cy5

description: Biological replicate 3 of 4.


title: CD630_WT2-Cy5_sigE2-Cy3

description: Biological replicate 2 of 4.


title: CD630_WT1-Cy5_sigE1-Cy3

description: Biological replicate 1 of 4.


title: CD630_WT1-Cy5_sigF1-Cy3

description: Biological replicate 1 of 4.


title: FliC1-WT1_Vivo

status: Public on Dec 31 2013

description:
Biological replicate 2 of 3.
raw data file: E_FliC-01_cy3-400_cy5-350.gpr

hyb_protocol: samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

scan_protocol: Scanned on an GenePix 4200L dual-channel laser scanner

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BY [statistical results provided as Series Supplementary file].

source_name: FliC mutant grown 14h in vivo

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C.difficile strains R20291 strain : a wild type strain, a fliC mutant and a fliC mutant complemented after 14h of growth in PY and a wild type strain and a fliC mutant after 14h of mouse infection in Vivo

extract_protocol: Total RNA extracted using RNAPro Blue (FastPrep) and following Qbiogen manufacturer's instructions

tag: strain background

value: fliC::erm (fliC mutant)

source_name: R20291 grown 14h in PY (reference)

value: wild type


title: FliC4-Comp4-WT4

description:
Biological replicate 4 of 4.
raw data file: FliC-Comp4-cy3-390_WT4-cy5-500.gpr

source_name: complemented FliC mutant grown 14H in PY

value: fliC::erm + pMTL84151 fliC (fliC mutant complemented)


title: FliC6-WT6_Vivo

description:
Biological replicate 1 of 3.
raw data file: H_FliC-06_cy3-290_cy5-420.gpr


title: FliC1-Comp1-WT1

description:
Biological replicate 1 of 4.
raw data file: FliC-Comp1-cy5-490_WT1-cy3-420.gpr


title: FliC3-Comp3-WT3

description:
Biological replicate 3 of 4.
raw data file: FliC-Comp3-cy3-390_WT3-cy5-490.gpr


title: FliC1-WT1

description:
Biological replicate 1 of 4.
raw data file: FliC1-cy5-490_WT1-cy3-360.gpr

source_name: FliC mutant grown 14H in PY


title: FliC3-WT3

description:
Biological replicate 3 of 4.
raw data file: FliC3-cy3-430_WT3-cy5-490.gpr


title: FliC2-WT2_Vivo

description:
Biological replicate 3 of 3.
raw data file: F_FliC-02_cy3-400_cy5-350.gpr


title: FliC2-WT2

description:
Biological replicate 2 of 4.
raw data file: FliC2-cy5-490_WT2-cy3-360.gpr


title: FliC2-Comp2-WT2

description:
Biological replicate 2 of 4.
raw data file: FliC-Comp2-cy5-490_WT2-cy3-430.gpr


title: 14h-02_Vivo

description:
Biological replicate 1 of 3.
raw data file: B_14h-02_cy3-350_cy5-400.gpr

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

data_processing: Background correction: backgroundCorrect 'normexp', Normalization: normalizeWithinArrays 'loess', Correlation of spot duplicat: duplicateCorrelation, Adjust to linear method: lmFit, Statistical analysis: eBayes, decideTests 'global' 'BY'[statistical results provided as Series Supplementary file].

source_name: R20291 extracted after 14h in vivo growth

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark. DNA samples were labelled using the Bioprime plus array CGH indirect genomic labeling system (invitrogen)

growth_protocol: We did a 9 hours preculture of Clostridium difficile R20291 in Tryptone yeast extract (TY), we centrifuged and resuspended in PBS. Then we gave 5ml of this preparation to 6 mouses  per time point (C. difficile monoxenic mouse model). Finally mouse were sacrificed, according European rules, at different time 4, 6, 8, 14 and 38 hours after infection to collect the luminal and mucosa associated bacteria in the caeca.

source_name: R20291 grown 14H in PY (reference)


title: 14h-05_Vivo

description:
Biological replicate 2 of 3.
raw data file: C_14h-05_cy3-290_cy5-420.gpr


title: 14h-06_Vivo

description:
Biological replicate 3 of 3.
raw data file: D_14h-06_cy3-290_cy5-420.gpr


title: CD-PYC04-cy5

description: Biological replicate 4 of 4.

data_processing:
R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.
VALUE column reports loess-normalized, log2 (test/reference) ratios.

source_name: strain C630E grown in PY with cysteine

growth_protocol: C.difficile strain C630E was grown for 10 hours in PY medium with 10 mM of cysteine or in PY corresponding to mild range contration of cysteine (Karolinska institut recipe)

extract_protocol: Total RNA extracted using RNAPro (FastPrep) and following MP manufacturer's instructions

tag: agent

value: 10 mM of cysteine

source_name: strain JIR8094 in TY 8H of growth (reference)


title: CD-PYC03-cy3

description: Biological replicate 3 of 4.


title: CD-PYC01-cy3

description: Biological replicate 1 of 4.


title: FliC4-WT4

description:
Biological replicate 4 of 4.
raw data file: FliC4-cy3-430_WT4-cy5-490.gpr


title: CD-PY02-cy5

description: Biological replicate 2 of 4.

source_name: strain C630E grown in PY

value: mild concentration of cysteine (control)


title: CD-PY04-cy5

description: Biological replicate 4 of 4.


title: C1_VITRO38H-cy5_VITRO8H-cy3

status: Public on Nov 04 2013

description:
in vitro 38h growth vs. in vitro 8h growth.
Biological replicate 1 of 2. Dye swap 2 of 2.

hyb_protocol: Samples were applied to microarrays enclosed in hybridization chambers in a water bath in the dark for 16-20h. After hybridization, slides were washed with washing buffers (http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=30&action=view).

scan_protocol: Scanned on a GenePix Pro 5 dual-channel laser scanner (ScanArray 4000).

source_name: strain 630E in TY 38H of growth

label_protocol: 10 µg of total RNA was used with a Genisphere 3DNA Array 900 MPX microarray kit for cDNA synthesis, labeling, and hybridization.

growth_protocol: C. difficile strain C630E was extracted after 8h, 14h and 38h in TY.

extract_protocol: Total RNA was extracted using the QIAgen RNeasy extraction kit.

tag: growth medium

value: TY

tag: time

value: 38h growth

source_name: strain 630E in TY 8H of growth (reference)

tag: culture medium

value: 8h growth


title: CD-PYC02-cy5

description: Biological replicate 2 of 4.

tag: strain

value: C630E Mullany


title: C2_VITRO38H-cy5_VITRO8H-cy3

description:
in vitro 38h growth vs. in vitro 8h growth.
Biological replicate 2 of 2. Dye swap 2 of 2.


title: CD-PY03-cy3

description: Biological replicate 3 of 4.


title: CD-PY01-cy3

description: Biological replicate 1 of 4.


title: C2_VITRO38H-cy3_VITRO8H-cy5

description:
in vitro 38h growth vs. in vitro 8h growth.
Biological replicate 2 of 2. Dye swap 1 of 2.


title: C2_VITRO14H-cy3_VITRO8H-cy5

description:
in vitro 14h growth vs. in vitro 8h growth.
Biological replicate 2 of 2. Dye swap 1 of 2.

source_name: strain 630E in TY 14H of growth

value: 14h growth


title: C2_VITRO14H-cy5_VITRO8H-cy3

description:
in vitro 14h growth vs. in vitro 8h growth.
Biological replicate 2 of 2. Dye swap 2 of 2.


title: VIVO38H2-cy5_VITRO8H-cy3

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 2 of 4. Dye swap 2 of 2.

source_name: Mouse10 38h after infection

growth_protocol: C. difficile strain C630E was extracted after 8h, 14h and 38h of an infection in mouse.

extract_protocol: RNA was extracted from the luminal content of mouse.

tag: host

value: mouse

value: 38h infection


title: C1_VITRO14H-cy3_VITRO8H-cy5

description:
in vitro 14h growth vs. in vitro 8h growth.
Biological replicate 1 of 2. Dye swap 1 of 2.


title: VIVO38H4-cy3_VITRO8H-cy5

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 4 of 4. Dye swap 1 of 2.

source_name: Mouse12 38h after infection


title: VIVO38H3-cy5_VITRO8H-cy3

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 3 of 4. Dye swap 2 of 2.

source_name: Mouse11 38h after infection


title: C1_VITRO38H-cy3_VITRO8H-cy5

description:
in vitro 38h growth vs. in vitro 8h growth.
Biological replicate 1 of 2. Dye swap 1 of 2.


title: VIVO38H1-cy5_VITRO8H-cy3

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 1 of 4. Dye swap 2 of 2.

source_name: Mouse9 38h after infection


title: C1_VITRO14H-cy5_VITRO8H-cy3

description:
in vitro 14h growth vs. in vitro 8h growth.
Biological replicate 1 of 2. Dye swap 2 of 2.


title: VIVO38H1-cy3_VITRO8H-cy5

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 1 of 4. Dye swap 1 of 2.


title: VIVO38H4-cy5_VITRO8H-cy3

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 4 of 4. Dye swap 2 of 2.


title: VIVO14H2-cy5_VITRO8H-cy3

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 2 of 4. Dye swap 2 of 2.

source_name: Mouse6 14h after infection

value: 14h infection


title: VIVO14H3-cy5_VITRO8H-cy3

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 3 of 4. Dye swap 2 of 2.

source_name: Mouse7 14h after infection


title: VIVO38H2-cy3_VITRO8H-cy5

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 2 of 4. Dye swap 1 of 2.


title: VIVO14H4-cy3_VITRO8H-cy5

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 4 of 4. Dye swap 1 of 2.

source_name: Mouse8 14h after infection


title: VIVO38H3-cy3_VITRO8H-cy5

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 3 of 4. Dye swap 1 of 2.


title: VIVO14H1-cy5_VITRO8H-cy3

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 1 of 4. Dye swap 2 of 2.

source_name: Mouse5 14h after infection


title: VIVO14H2-cy3_VITRO8H-cy5

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 2 of 4. Dye swap 1 of 2.


title: VIVO14H3-cy3_VITRO8H-cy5

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 3 of 4. Dye swap 1 of 2.


title: VIVO14H4-cy5_VITRO8H-cy3

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 4 of 4. Dye swap 2 of 2.


title: VIVO14H1-cy3_VITRO8H-cy5

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 1 of 4. Dye swap 1 of 2.


title: VIVO8H3-cy5_VITRO8H-cy3

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 3 of 4. Dye swap 2 of 2.

source_name: Mouse3 8h after infection

value: 8h infection


title: VIVO8H4-cy5_VITRO8H-cy3

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 4 of 4. Dye swap 2 of 2.

source_name: Mouse4 8h after infection


title: VIVO8H2-cy5_VITRO8H-cy3

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 2 of 4. Dye swap 2 of 2.

source_name: Mouse2 8h after infection


title: VIVO8H1-cy5_VITRO8H-cy3

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 1 of 4. Dye swap 2 of 2.

source_name: Mouse1 8h after infection


title: VIVO8H2-cy3_VITRO8H-cy5

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 2 of 4. Dye swap 1 of 2.


title: VIVO8H3-cy3_VITRO8H-cy5

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 3 of 4. Dye swap 1 of 2.


title: VIVO8H1-cy3_VITRO8H-cy5

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 1 of 4. Dye swap 1 of 2.


title: CD630_WT-cy5_sigD6-cy3

status: Public on Aug 31 2013

description: Biological replicate 4 of 4.

scan_protocol: Scanned on an GenePix Pro 6 dual-channel laser scanner

source_name: strain C630E grown 6h in BHI (reference)

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C.difficile strain C630E was grown for 6 hours in BHI medium.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen)

source_name: sigD mutant grown 6h in TY

value: sigD mutant


title: VIVO8H4-cy3_VITRO8H-cy5

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 4 of 4. Dye swap 1 of 2.


title: MCF7 + AMD3100 + estrogen

status: Public on Dec 21 2012

description: MCF7 + AMD3100 + estrogen

data_processing: gcRMA; software was R using Bioconductor packages.

source_name: MCF7 + AMD3100 + estrogen

label_protocol: GeneChip 3? IVT Express kits (Affymetrix) were used to amplify cRNA from 500 ng total RNA.

extract_protocol: Total RNA was isolated from cell pellets using the RNeasy kit (Qiagen, Valencia, CA, USA)

treatment_protocol: Estrogen pellets, 1.7 mg/90 days release;AMD3100: 25 mg/ml, 0.25 ul/h release

tag: cell line

value: AMD3100 + estrogen


title: MCF7 + estrogen

description: MCF7 + estrogen

source_name: MCF7 + estrogen

treatment_protocol: Estrogen pellets, 1.7 mg/90 days release

value: estrogen


title: CD630_WT-cy3_sigD5-cy5

description: Biological replicate 3 of 4.


title: MCF7(TAM-R) + AMD3100 + estrogen

description: MCF7(TAM-R) + AMD3100 + estrogen

source_name: MCF7(TAM-R) + AMD3100 + estrogen


title: CD630_WT-cy3_sigD1-cy5

description: Biological replicate 1 of 4.


title: CD630_WT-cy3_sigD3-cy5

description: Biological replicate 2 of 4.


title: ccpA_TY1-cy3

status: Public on Oct 02 2012

description: Biological replicate 1 of 4.

source_name: Mutant ccpA CD630E JIR8094 10H in TY

growth_protocol: C.difficile strains CD630E JIR8094, a WT and a mutant ccpA strains, were grown for 10 hours in TY

tag: genotype

tag: treatment

value: 10H in TY

source_name: CD630E JIR8094 in TY 8H of growth (reference)

value: 8H in TY


title: WT3-cy5_ccpA3-cy3

type: genomic

description:
Raw data file: WT3-cy5_ccpA3-cy3.gpr
Biological replicate 3 of 3.

molecule: genomic DNA

source_name: strain JIR8094 (CD630E) grown 6h in TYG (reference)

label_protocol: DNA samples were labelled using the Bioprime plus array CGH indirect genomic labeling system (invitrogen)

growth_protocol: C.difficile strains were grown for 6 hours in TYG medium.

extract_protocol: Formaldehyde 1% 10min, Glycine 400mM, Centrifugation, IP buffer, Sonication, Immunoprecipitation using ccpA antibodies and Pan mouse immunoglobulin G magnetic beads, proteinase K, DNA purification kit.

tag: genotype/variation

value: wild type

tag: chip antibody

value: anti-ccpA antibody (made in-house)

source_name: ccpA mutant grown 6h in TYG (test)

value: ccpA mutant


title: ccpA_TY4-cy5

description: Biological replicate 4 of 4.


title: WT2-cy3_ccpA2-cy5

description:
Raw data file: WT2-cy3_ccpA2-cy5.gpr
Biological replicate 2 of 3.


title: MCF7(TAM-R) + estrogen

description: MCF7(TAM-R) + estrogen

source_name: MCF7(TAM-R) + estrogen


title: WT1-cy3_ccpA1-cy5

description:
Raw data file: WT1-cy3_ccpA1-cy5.gpr
Biological replicate 1 of 3.

source_name: strain C630E grown 6h in TYG (reference)


title: MCF7 + tamoxifen

description: MCF7 + tamoxifen

source_name: MCF7 + tamoxifen

treatment_protocol: athymic nude mice with implanted xenografts were treated with 500 ug tamoxifen 5 days per week

value: tamoxifen


title: ccpA_TY2-cy5

description: Biological replicate 2 of 4.


title: MCF7(TAM-R) + AMD3100 + tamoxifen

description: MCF7(TAM-R) + AMD3100 + tamoxifen

source_name: MCF7(TAM-R) + AMD3100 + tamoxifen

treatment_protocol: athymic nude mice with implanted xenografts were treated with 500 ug tamoxifen 5 days per week, and AMD3100: 25 mg/ml, 0.25 ul/h release

value: AMD3100 + tamoxifen


title: WT_TY2-cy5

description: Biological replicate 2 of 4.

source_name: CD630E JIR8094 10H in TY


title: WT_TY3-cy3

description: Biological replicate 3 of 4.


title: WT_TY1-cy3

description: Biological replicate 1 of 4.


title: ccpA_TYG4-cy5

description: Biological replicate 4 of 4.

source_name: Mutant ccpA CD630E JIR8094 10H in TY with 0.5% glucose

growth_protocol: C.difficile strains CD630E JIR8094, a WT and a mutant ccpA strains, were grown for 10 hours in TY with 0.5% glucose

value: 10H in TY with 0.5% glucose


title: ccpA_TYG1-cy3

description: Biological replicate 1 of 4.


title: WT_TY4-cy5

description: Biological replicate 4 of 4.


title: MCF7 + AMD3100 + tamoxifen

description: MCF7 + AMD3100 + tamoxifen

source_name: MCF7 + AMD3100 + tamoxifen


title: MCF7(TAM-R) + tamoxifen

description: MCF7(TAM-R) + tamoxifen

source_name: MCF7(TAM-R) + tamoxifen


title: ccpA_TYG3-cy3

description: Biological replicate 3 of 4.


title: WT_TYG4-cy5

description: Biological replicate 4 of 4.

source_name: CD630E JIR8094 10H in TY with 0.5% glucose


title: ccpA_TY3-cy3

description: Biological replicate 3 of 4.


title: ccpA_TYG2-cy5

description: Biological replicate 2 of 4.


title: WT_TYG2-cy5

description: Biological replicate 2 of 4.


title: WT_TYG3-cy3

description: Biological replicate 3 of 4.


title: WT_TYG1-cy3

description: Biological replicate 1 of 4.


title: GFPMYC negative GC B cells, Biological replicate 3

status: Public on Sep 24 2012

city: New York

first: David

last: Dominguez-Sola

state: NY

address: One Gustave L. Levy Place, Box 1044A

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
Sample name: GFPMYCneg_10G
Gene expression data from MYC negative GC B cell subpopulation, paired to 9G

hyb_protocol: 3.75 micrograms of fragmented, Biotin-labeled amplified cDNA was hybridized using the Affymetrix HWS kit, Standard Array (49 Format), using NuGEN's Encore Biotin kit instructions. Samples were hybridized for 16 hours. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G, connected to Command Console software.

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

source_name: Spleen, SRBC immunized mouse, 12 days post-immunization

label_protocol: Encore Biotin Labeling Kit (NuGEN). Biotin labeled and fragmented amplified cDNA was prepared following manufacturer's instructions.

growth_protocol: 8 week old GFPMYC/C57BL6 mouse, Sheep Red Blood Cell (SRBC) immunization, 12 days

extract_protocol: Sorted GC B cells. Total RNA isolated using Nucleospin RNA XS kit (Macherey Nagel). cDNA was amplified from 5-20 ng of total RNA using the Ovation RNA amplification kit (NuGEN), following manufacturer's instructions.

treatment_protocol: B cell fraction was isolated using magnetic beads (B cell isolation kit, Miltenyi). GC B cells (PNAhi/CD95hi) were sorted based on their relative GFP(=MYC) expression in two pools (MYC+, MYC-) for each mouse

tag: tissue

value: Spleen

tag: cell type

value: B lymphocytes

tag: gfpmyc status

value: negative


title: GFPMYC positive GC B cells, Biological replicate 5

description:
Sample name: GFPMYCpos_11G
Gene expression data from MYC positive GC B cell subpopulation, paired to 12G

value: positive


title: Kartogenin_10nM_24h

status: Public on May 02 2012

data_processing: gcRMA using R version 2.8.0 (2008-10-20).

extract_protocol: Total RNA was isolated from cell pellets using Trizol extraction followed by clean up with an RNeasy kit (Qiagen, Valencia, CA, USA)

treatment_protocol: Bone marrow derived human mesenchymal stem cells were purchased from All Cells (Emeryville, CA, USA). Cells were plated in 6 well dishes in growth media. Once adhered,   the media was changed to serum free DMEM and treated with either DMSO or Kartogenin (100nM, 10nM, or 1nM) for 6 or 24 hours.   At the indicated time points, the media was removed, the cells scraped in PBS, centrifuged briefly, the PBS removed and the pellet frozen at -80C until RNA isolation.

value: human mesenchymal stem cells


title: GFPMYC positive GC B cells, Biological replicate 7

description:
Sample name: GFPMYCpos_1G
Gene expression data from MYC positive GC B cell subpopulation, paired to 2G


title: GFPMYC positive GC B cells, Biological replicate 6

description:
Sample name: GFPMYCpos_9G
Gene expression data from MYC positive GC B cell subpopulation, paired to 10G


title: GFPMYC negative GC B cells, Biological replicate 4

description:
Sample name: GFPMYCneg_2G
Gene expression data from MYC negative GC B cell subpopulation, paired to 1G


title: GFPMYC positive GC B cells, Biological replicate 4

description:
Sample name: GFPMYCpos_7G
Gene expression data from MYC positive GC B cell subpopulation, paired to 8G


title: GFPMYC negative GC B cells, Biological replicate 2

description:
Sample name: GFPMYCneg_12G
Gene expression data from MYC negative GC B cell subpopulation, paired to 11G


title: CD630_sigH4-cy5_WT4-cy3

status: Public on Aug 22 2011

description: Biological replicate 4 of 4.

source_name: strain C630E grown 10h in TY (reference)

growth_protocol: C.difficile  630E strain 10h vs sigH mutant 10h grown for 10 hours in TY medium.

value: C630E Mullany

source_name: sigH mutant grown 10h in TY (test)

value: sigH mutant


title: CD630_sigH2-cy5_WT2-cy3

description: Biological replicate 2 of 4.


title: Kartogenin_100nM_6h


title: Kartogenin_1nM_24h


title: CD630_sigH1-cy3_WT1-cy5

description: Biological replicate 1 of 4.


title: DMSO

description: DMSO

source_name: DMSO


title: Kartogenin_1nM_6h


title: GFPMYC negative GC B cells, Biological replicate 1

description:
Sample name: GFPMYCneg_8G
Gene expression data from MYC negative GC B cell subpopulation, paired to 7G


title: Kartogenin_10nM_6h


title: CD630_WT2-10h-cy5_WT2-4h-cy3

description: Biological replicate 2 of 4.

source_name: strain C630E grown 4h in TY (test)

growth_protocol: C.difficile strain C630E was grown for 4h or 10 hours in TY medium.

source_name: strain 630E in TY 10H of growth (reference)


title: CD630_sigH3-cy3_WT3-cy5

description: Biological replicate 3 of 4.


title: CD630_WT4-10h-cy5_WT4-4h-cy3

description: Biological replicate 4 of 4.


title: CD630_WT3-10h-cy3_WT3-4h-cy5

description: Biological replicate 3 of 4.


title: homozygous_TGFb_24hr_1

status: Public on Jul 11 2011

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures using GCS3000 scanner

data_processing: gcRMA, unlogged

label_protocol: 2 ug total RNA was used in a standard Affymetrix single amplification protocol.

extract_protocol: Total RNA was isolated from cell pellets using the RNeasy kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Mouse embryonic fibroblasts (MEF) cells were harvested as described. Briefly, timed pregnancies were set up; E12.5 to E14.5 fetuses were harvested. After carefully removing the embryo’s head, liver and blood clots, the rest of the tissues were washed with PBS, minced and digested with Trypsin at 37?C for 10 min. After digestion, fetal tissues were vigorously pipetted until it is a single cell suspension. The cells were spun down and cultured in DMEM supplemented with Gentamicin, Glutamine, non-essential amino acids, 2-mercaptoethanol and 10% FBS at 37 ?C in a 5% CO2 incubator.  MEFs with 3 different genotypes were treated with or without 5 ng/mL TGF-b1 (R&D systems) for indicated times.


title: homozygous_TGFb_4hr_1


title: homozygous_1


title: Kartogenin_100nM_24h


title: CD630_WT1-10h-cy3_WT1-4h-cy5

description: Biological replicate 1 of 4.


title: heterozygous_TGFb_4hr_1


title: homozygous_2


title: heterozygous_2


title: homozygous_TGFb_24hr_2


title: heterozygous_TGFb_24hr_2


title: heterozygous_TGFb_24hr_1


title: wt_TGFb_24hr_1


title: wt_2


title: wt_TGFb_24hr_2


title: wt_TGFb_4hr_2


title: heterozygous_1


title: heterozygous_TGFb_4hr_2


title: homozygous_TGFb_4hr_2


title: LGC006_1000nM_24hr

status: Public on Apr 04 2011

data_processing: gcRMA

extract_protocol: RNA extraction was performed by using RNeasy kits(Qiagen). The integrity and concentration of RNA was determined by microfluidic analysis on an Experion instrument (BioRad)

treatment_protocol: mPB CD34+ cells treated with compounds at the indicated time points

value: hematopoietic stem cell (HSC)

tag: dose


title: LGC006_30nM_24hr


title: wt_1


title: wt_TGFb_4hr_1


title: SR1_30nM_24hr


title: LGC006_300nM_24hr


title: SR1_0nM_24hr


title: SR1_300nM_24hr


title: CP-CymR02-cy3

status: Public on Oct 01 2010

description: Biological replicate 2 of 4

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed in Agilent washing buffers.

scan_protocol: Scanned on an GenePix 4200L dual-channel laser scanner.

organism: Clostridium perfringens

source_name: strain 13∆cpe1786 erm grown with cystine

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), and each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C. perfringens strains were grown in minimal medium in the presence of 0.5 mM cystine until late exponential growth phase.

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

tag: genome/variation

value: ∆cpe1786 erm

source_name: strain 13 grown with cystine


title: SR1_100nM_24hr


title: SR1_1000nM_24hr


title: CP-CymR01-cy5

description: Biological replicate 1 of 4


title: 1_uM_retinoic_acid_forskolin_

status: Public on Aug 18 2010

hyb_protocol: Standard Affymetrix protocols were used to process Affymetrix rat genome 230_2 microarrays (Affymetrix).

data_processing: CEL files were processed using the "full model" of GCRMA (Wu Z, Irizarry RA: Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol 2005, 12(6):882-893.) and R version 2.6.2.  GCRMA and associated packages were downloaded from Bioconductor (www.bioconductor.org).  GCRMA output was unlogged.

organism: Rattus norvegicus

label_protocol: GeneChip 3' IVT Express kits (Affymetrix) were used to amplify cRNA from 5 ug total RNA.

extract_protocol: RNeasy kits (Qiagen) were used to extract total RNA from DMSO- or compound-treated NPCs. The integrity and concentration of RNA were determined via microfluidic analysis on an Experion instrument (BioRad).

treatment_protocol: Rat NPCs were derived and cultured as described previously by others. After hippocampal cell isolation, the number of dissociated cells was determined and 5 × 105 cells were plated in 60-mm uncoated plates. After overnight incubation (37 °C, 5% CO2, and 95% humidity), the medium was changed and the cells were expanded and maintained in an undifferentiated state on polyornithine- (10 ug/mL in water; Sigma) and laminin-coated (5 ug/mL in PBS; Invitrogen) dishes in DMEM/F12 (Invitrogen) supplemented with N2 (Invitrogen) and basic fibroblast growth factor (bFGF, 20 ng/mL; Invitrogen). For KHS101 and shRNA-induction experiments, early passage cells (passaged no more than six times after hippocampal isolation) were trypsinized and plated at a density of 1,000 cells/cm2 into N2 medium (DMEM/F12 supplemented with N2) containing KHS analogs (e.g., KHS101, KHS92, and NP) at different concentrations (0.5-5 uM) or DMSO(0.1%), RA (1-2 uM), BDNF (100 ng/mL), and/or BMP4 (50-100 ng/mL) for 4 d.

value: Fisher 344

value: hippocampal progenitor cells


title: DMSO

description: DMSO

value: DMSO


title: 28C: Letrozole, 2.5mg/day,oral, 90 days; responder

status: Public on Jul 28 2010

description: breast tumor biopsy

hyb_protocol: standard Affymetrix procedures except for use of a custom 24-channel fluidics machine

label_protocol: Approximately 500 ng of total RNA was processed to produce biotinylated cRNA targets using protocol described in Biotechniques. 2003 Mar;34(3):546-50, 552-4, 556

extract_protocol: Biopsies were snap-frozen after collection and stored in liquid nitrogen.  Frozen sections were taken prior to RNA extraction to confirm the presence of cancerous tissue within the specimens.  Only samples in which the malignant component comprised at least 20% of the section area were used in further analyses.  Immediately before RNA extraction the biopsies were pulverised using U2 micro-dismembranator U (Braun Biotech).  Total RNA was extracted from the resultant frozen tissue powder using TRI-reagent (Sigma) according to the manufacturer's recommendations.  Extracted RNA was additionally purified on RNeasy mini columns (Qiagen).  RNA quantity and quality was verified on Bioanalyser 2100 (Agilent).

treatment_protocol: breast biopsies were taken from subjects after 90 days Letrozol, 2.5 mg

tag: subject

tag: gender

value: female

value: breast tumor

value: Letrozol

tag: administration

value: oral

value: 90 days


title: 27C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy

tag: agent

tag: time


title: 9C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: GBM_stem_F_shRNA_B9

status: Public on Mar 14 2011

extract_protocol: RNeasy kits (Qiagen) were used to extract total RNA from brain tumor initiating cells. The integrity and concentration of RNA was determined via microfluidic analysis on an Experion instrument (BioRad).

treatment_protocol: Microarray expression analysis of shTR1- and shTR2-expressing GBM-1 knockdown cells compared to non-targeting shRNA-expressing control cells TRRAP (shTR1, target sequence: CGTGTAAGAAAGGGAGAATAT; shTR2, target sequence: GCCCTGTTCTTTCGCTTTGTA). Total RNA for each sample was obtained after short term puromycin selection (5 ug/mL for 2 days followed by 1 ug/mL for 2 days) from two independent lentiviral infections and pooled prior to RNA preparation.

value: shTR2-mediated TRRAP knockdown


title: 22C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 25C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: CP-CymR03-cy3

description: Biological replicate 3 of 4

tag: strain

value: wild type


title: 16C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: CP-CymR04-cy3

description: Biological replicate 4 of 4


title: CP-CymR02-cy5

description: Biological replicate 2 of 4


title: CP-CymR03-cy5

description: Biological replicate 3 of 4


title: GBM_stem_A_BMP_shRNA_B8

value: shTR1-mediated TRRAP knockdown


title: CP-CymR04-cy5

description: Biological replicate 4 of 4


title: 12C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 7C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: GBM_stem_A_control

value: control


title: 24C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: CP-CymR01-cy3

description: Biological replicate 1 of 4


title: 1.7_uM_KHS_101


title: 20C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 5_uM_KHS_101


title: 14C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 15C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 10C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 17C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 18C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 8C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 23C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 21C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 13C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 60C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 19C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 65C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 11C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 63C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 64C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 59C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 57C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 69C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 58C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 67C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 50C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 53C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 68C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 52C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 47C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 55C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 45C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 49C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 41C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 46C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 43C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 39C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 36C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 42C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 44C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 51C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 37C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 34C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 31C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 40C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 29C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 35C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 2C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: 33C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: 4C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 3C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 6C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy


title: 30C: Letrozole, 2.5mg/day,oral, 90 days; nonresponder

description: breast tumor biopsy


title: CP-Hcys04-cy5

status: Public on Jun 01 2010

description: Biological replicate 4 of 4

source_name: strain 13 grown in the presence of homocysteine

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C. perfringens strain 13 was grown in minimal medium in the presence of 1 mM homocysteine or 0.5 mM cystine until late exponential growth phase.

tag: growth protocol

value: 1 mM homocysteine

source_name: strain 13 grown in the presence of cystine

value: 0.5 mM cystine


title: 5C: Letrozole, 2.5mg/day,oral, 90 days; responder

description: breast tumor biopsy


title: CP-Hcys02-cy3

description: Biological replicate 2 of 4


title: CP-Hcys04-cy3

description: Biological replicate 4 of 4


title: CP-Hcys01-cy3

description: Biological replicate 1 of 4


title: CP-Hcys03-cy3

description: Biological replicate 3 of 4


title: CP-Hcys02-cy5

description: Biological replicate 2 of 4


title: CP-Hcys03-cy5

description: Biological replicate 3 of 4


title: CP-Hcys01-cy5

description: Biological replicate 1 of 4


title: amygdala 92

status: Public on May 08 2009

description: amygdala

data_processing: RMA

source_name: amygdala

label_protocol: 2 ug total RNA was used with the GeneChip WT Sense Target Labeling Kit

extract_protocol: Total RNA was isolated from cell pellets using Trizol (Invitrogen, Carlsbad, CA) followed by clean up using the RNeasy kit (Qiagen, Valencia, CA, USA).

treatment_protocol: RNA extraction from tissues of naïve male (except females for specific organs) C57BL/6J mice, 8-10 weeks of age

value: amygdala


title: hippocampus 100

description: hippocampus

source_name: hippocampus

value: hippocampus


title: hippocampus 99

description: hippocampus


title: umbilical cord 102

value: umbilical cord


title: mammary gland lactating 103

value: mammary gland  lact


title: adipose white 93

value: adipose white


title: epidermis 90

description: epidermis

source_name: epidermis

value: epidermis


title: placenta 106

description: placenta

source_name: placenta

value: placenta


title: placenta 105

description: placenta


title: amygdala 91

description: amygdala


title: umbilical cord 101


title: adrenal gland 95

value: adrenal gland


title: epidermis 89

description: epidermis


title: adipose white 94


title: lung 87

description: lung

source_name: lung

value: lung


title: liver 86

description: liver

source_name: liver

value: liver


title: spinal cord 80

value: spinal cord


title: uterus 84

description: uterus

source_name: uterus

value: uterus


title: liver 85

description: liver


title: adrenal gland 96


title: pancreas 82

description: pancreas

source_name: pancreas

value: pancreas


title: mammary gland lactating 104


title: pancreas 81

description: pancreas


title: bone 97

description: bone

source_name: bone

value: bone


title: uterus 83

description: uterus


title: lung 88

description: lung


title: bone marrow 77

value: bone marrow


title: bone 98

description: bone


title: RAW 264 7 73

tag: cell line


title: C3H/10T1/2 76


title: bone marrow 78


title: spinal cord 79


title: RAW 264 7 74


title: neuro2a 70


title: nih 3T3 72

value: nih 3T3


title: C3H/10T1/2 75


title: neuro2a 69


title: nih 3T3 71


title: mIMCD-3 67


title: min6 66


title: C2C12 63


title: 3T3-L1 59


title: 56C: Letrozole, 2.5mg/day,oral, 90 days; not assessable

description: breast tumor biopsy

value: female

value: breast tumor

value: Letrozol

value: oral

value: 90 days


title: mIMCD-3 68


title: macrophage bone marrow 24hr hr LPS 57

value: macrophage bone marrow 24hr hr LPS


title: Baf3 61


title: 3T3-L1 60


title: min6 65


title: macrophage bone marrow 2hr LPS 54

value: macrophage bone marrow 2hr LPS


title: Baf3 62


title: macrophage bone marrow 6hr LPS 56

value: macrophage bone marrow 6hr LPS


title: C2C12 64


title: macrophage bone marrow 2hr LPS 53


title: macrophage bone marrow 24hr hr LPS 58


title: embryonic stem cell line V26 2 p16 50

value: embryonic stem cell line V26 2 p16


title: embryonic stem cell line V26 2 p16 49


title: macrophage bone marrow 6hr LPS 55


title: mammary gland non-lactating 40

value: mammary gland non-lactating


title: macrophage bone marrow 0hr 52

value: macrophage bone marrow 0hr


title: macrophage peritoneal LPS thioglycollate 7hrs 46

description: macrophage_peritoneal_LPS_thioglycollate_7hrs


title: macrophage bone marrow 0hr 51


title: AMB_200609_9mo_5E_6E_1_P5-6-N18-G11

status: Public on Dec 18 2025

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: age

value: 9 months

tag: brain region

value: CP

value: M


title: macrophage peritoneal LPS thioglycollate 1hrs 43

description: macrophage_peritoneal_LPS_thioglycollate_1hrs


title: adipose brown 29

value: adipose brown


title: adipose brown 30


title: embryonic stem cell line Bruce4 p13 48

value: embryonic stem cell line Bruce4 p13


title: pituitary 35

description: pituitary

source_name: pituitary

value: pituitary


title: macrophage peritoneal LPS thioglycollate 0hrs 41

description: macrophage_peritoneal_LPS_thioglycollate_0hrs


title: dorsal root ganglia 34

value: dorsal root ganglia


title: heart 27

description: heart

source_name: heart

value: heart


title: mammary gland non-lactating 39


title: macrophage peritoneal LPS thioglycollate 1hrs 44


title: dorsal root ganglia 33


title: testis 37

description: testis

source_name: testis

value: testis


title: embryonic stem cell line Bruce4 p13 47


title: olfactory bulb 31

value: olfactory bulb


title: macrophage peritoneal LPS thioglycollate 7hrs 45


title: testis 38

description: testis


title: heart 28

description: heart


title: intestine small 22

value: intestine small


title: intestine small 21


title: hypothalamus 25

description: hypothalamus

source_name: hypothalamus

value: hypothalamus


title: pituitary 36

description: pituitary


title: stomach 23

description: stomach

source_name: stomach

value: stomach


title: prostate 17

description: prostate

source_name: prostate

value: prostate


title: spleen 20

description: spleen

source_name: spleen

value: spleen


title: stomach 24

description: stomach


title: spleen 19

description: spleen


title: olfactory bulb 32


title: BayK8644(2a)_Exendin-4_24h

status: Public on Jan 19 2009

label_protocol: 5 ug total RNA was used in a standard Affymetrix single amplification protocol.

extract_protocol: Total RNA was isolated from cell pellets using the RNeasy kit (Qiagen, Valencia, CA, USA). The integrity and concentration of RNA was determined by microfluidic analysis on an Experion instrument (BioRad).

treatment_protocol: R7T1 beta-cells treated with compounds at the indicated time points


title: kidney 8

description: kidney

source_name: kidney

value: kidney


title: BayK8644(2a)_Exendin-4_30min


title: kidney 9

description: kidney


title: BayK8644(2a)_Exendin-4_2h


title: Exendin-4_2h


title: Exendin-4_30min


title: BayK8644(2a)_24h


title: lymph nodes 13

value: lymph nodes


title: intestine large 11

value: intestine large


title: Exendin-4_6h


title: DMSO_6h


title: skeletal muscle 18

value: skeletal muscle


title: BayK8644(2a)_6h


title: intestine large 10


title: bladder 1

description: bladder

source_name: bladder

value: bladder


title: cerebellum 2

description: cerebellum

source_name: cerebellum

value: cerebellum


title: BayK8644(2a)_2h


title: lymph nodes 12


title: BayK8644(2a)_30min


title: cerebral cortex 4

value: cerebral cortex


title: DMSO_2h


title: 3PPS07042003_DU145_cell_monolayer

status: Public on Dec 09 2008

data_processing: gcRMA, scaled to a median intensity of 100

label_protocol: 50 ng total RNA was used in a standard Affymetrix double amplification protocol.

treatment_protocol: For flow cytometry, cell were dissociated with Accutase (Innovative Cell Tech Inc., San Diego, CA, USA) and washed 2 times in the staining solution containing Ca2+ and Mg2+-free PBS with 1mM ethylenediaminetetraacetic acid (EDTA), 25mM Hepes (pH 7.0) (Gibco BRL), 0.5% FBS. Cells were stained live in the staining solution containing conjugated anti-CD44 and anti-CD133 antibody (50 min at 4oC). Samples were analyzed on BD LSR II flow cytometer (Beckton Dickinson Immunocytometry Systems, San Jose, CA).  A minimum of (or At least) 500,000 viable cells were measured per sample. For FACS, 2x107 cells were processed for double CD44 and CD133 staining along with appropriate negative controls and single color positive controls. The CD44+/CD133+ and CD44-/CD133- populations were sorted out on a BD FACS Diva cell sorter (Beckton Dickinson Immunocytometry Systems, San Jose, CA).


title: ovary 14

description: ovary

source_name: ovary

value: ovary


title: DMSO_24h


title: BayK8644(2a)_Exendin-4_6h


title: DMSO_30min


title: 3PPS07042002_PC3_cell_spheres


title: 3PPS07042001_PC3_cell_monolayer


title: mast cells

status: Public on May 05 2008

description: mast cells

hyb_protocol: standard Affymetrix procedures except for use of custom GNF chip washer

source_name: mast cells

treatment_protocol:
Bone marrow cells from tibias, femurs and hip bones from 8-10 week old C57BL/6 mice were harvested, lysed with 1x ammonium chloride lysing reagent (PharMlyse BD cat# 555899) for 5 minutes and resuspended  with RPMI medium  (Mediatech, Inc.) supplemented with 10% FBS (Hyclone), 100 U/ml penicillin G, 100 U/ml streptomycin, and 292 ?g/ml of l-glutamine, 10 mM Hepes (pH 7.4),
0.1 mM nonessential amino acid, 1 mM sodium pyruvate, and 50 uM 2-mercaptoethanol with SCF (50 ng/ml) and IL-3–conditioned medium (final concentration of IL3 was 25 ng/ml).  During the first 2-3 weeks of culture the medium was changed every 3 days, and the cells were transferred to new dishes to separate them from adherent cells. Cells were cultured for another 6-8 weeks with media change once a week until BMMC reach full differentiation.
Mature mast cells are determined by FACS confirmation of c-Kit and FceR1 expression in >95% of the cell population containing double positives for both receptors.  WEHI-3 cells were obtained from ATCC and were used as a source of IL3 to supplement the BMMC growth medium .  WEHI-3 cells were cultured in IMDM containing 1.5g/L sodium bicarbonate, 100U/ml pen/strep, 1% L-glutamine,  0.05 mM 2-mercaptoethanol, and 10% FBS.

tag: mast cells


title: macrophage_7hrLPS rep 2

treatment_protocol:
Specific, homogenous bone marrow-derived macrophages (BMM) were obtained by ex vivo differentiation from mouse bone marrow progenitors in the presence of recombinant CSF1 as described previously ( Tushinski, R. J., I. T. Oliver, L. J. Guilbert, P. W. Tynan, J. R. Warner, and E. R. Stanley. 1982.
Survival of mononuclear phagocytes depends on a lineage-specific growth factor that the differentiated cells selectively destroy. Cell 28:71-81; Hume, D. A., and S. Gordon. 1983. Optimal conditions for proliferation of bone marrow-derived mouse macrophages in culture: the roles of CSF-1, serum, Ca2+, and adherence. J Cell Physiol 117:189-194).
All mice were specific pathogen free (SPF), male and 6 to 8 weeks old at the time of bone marrow collection. The femoral and/or tibial bone was extracted, remaining muscle removed and the bone sterilised in 70% ethanol.  The bone cavity was flushed with a 27-gauge needle using complete media (RPMI 1640 supplemented with 5 to 10% fetal bovine serum, 20 U/ml penicillin and 20 ug/ml streptomycin, 2 mM L-glutamine.
The pooled bone marrow progenitors were cultured on bacteriological plastic at two to six plates per bone.  Media was replaced on day five and cells re-seeded at day six onto tissue culture plastic. Cells were stimulated with lipopolysaccharide (LPS, Sigma) early on day seven and harvested over a time course (0, 1, 7h). Cells were harvested and RNA extracted using an  RNeasy kit (Qiagen), according to manufacturer’s instructions.


title: mast cells rep 2

description: mast cells


title: macrophage_7hrLPS


title: cerebral cortex prefrontal 6

value: cerebral cortex prefrontal


title: cerebral cortex 5


title: macrophage peritoneal LPS thioglycollate 0hrs 42


title: prostate 16

description: prostate


title: cerebral cortex prefrontal 7


title: hypothalamus 26

description: hypothalamus


title: SPRET/EiJ

status: Public on May 01 2008

description: epididymal fat was taken from 2 25-week old males and pooled

source_name: SPRET/EiJ

label_protocol: Three micrograms of total RNA was processed to produce biotinylated cRNA targets using standard Affymetrix procedures

extract_protocol: Samples were taken from epididymal fat and frozen on dry ice.  Frozen tissues were individually pulverized.  Total RNA was extracted from the resultant frozen tissue powder using TRI-reagent (Sigma) according to the manufacturer's recommendations.  Extracted RNA was additionally purified on RNeasy mini columns (Qiagen).  RNA quantity and quality was verified on Bioanalyser 2100 (Agilent).  For each strain, RNA was pooled so that the final amount was 3 micrograms total RNA, with each mouse represented in equal proportions.  The number of mice pooled per strain is noted under the Sample Description section.

tag: SPRET/EiJ


title: macrophage_1hrLPS


title: macrophage_unstimulated rep 2


title: macrophage_unstimulated


title: osteoclasts rep 2

description: osteoclasts

source_name: osteoclasts

treatment_protocol:
Bone marrow cells were harvested and washed in the same manner as used for BMM preparation, except that DMEM was substituted for RPMI-1640.
The cells were resuspended for differentiation in DMEM+Pen/Strep+Glutamax+10% heat inactivated FCS with 50 µg/mL ascorbic acid + 20 ng/mL human soluble RANKL (Peprotech) + 1 x 104 U/mL human soluble CSF-1 (Cetus). Medium was changed on day 3 and day 6, and cells were harvested for RNA on day 7.
Medium was changed on day 3 and day 6, and cells were harvested for RNA on day 7.

tag: osteoclasts


title: osteoclasts

description: osteoclasts


title: WSB/EiJ

description: epididymal fat was taken from 3 25-week old males and pooled

source_name: WSB/EiJ

tag: WSB/EiJ


title: osteoblasts_day14 rep 2

treatment_protocol:
Primary osteoblast cells were isolated by 10-minute sequential digestion of 2 day-old (specific pathogen free) neonatal C57BL/6 calvaria with 0.25 U/ml collagenase D (Roche Diagnostics, Indianapolis, IN, USA) and 2.2 U/ml dispase (Invitrogen, Carlsbad, CA, USA).  Digest fractions 2 to 6 were pooled as primary calvarial osteoblasts.
Osteoblasts were cultured in complete MEM media supplemented with 10% heat-inactivated FBS, 20 U/mL penicillin, 20 ug/mL streptomycin and 2 mM L-glutamine (Invitrogen).  Osteoblasts were differentiated in complete BGJb media supplemented with 10% heat-inactivated FBS, 20 U/mL penicillin, 20 ?g/mL streptomycin and 2 mM L-glutamine (Invitrogen) with 50 ?g/ml of ascorbate acid (Sigma-Aldrich, St Louis, MO, USA) and 10 mM ?-glycerophosphate (Sigma-Aldrich) from day 7 of culture.
Cells were harvested on day 5 (proliferation phase), day 14 (differentiation phase) and day 21 (mineralization phase) representing different stages of osteoblast differentiation and RNA was extracted using an RNeasy kit (Qiagen), according to manufacturer’s instructions.


title: osteoblasts_day21


title: osteoblasts_day5


title: osteoblasts_day21 rep 2


title: osteoblasts_day5 rep 2


title: 3PPS07042004_DU145_cell_spheres


title: SWR/J

source_name: SWR/J

tag: SWR/J


title: osteoblasts_day14


title: Exendin-4_24h


title: macrophage_1hrLPS rep 2


title: SM/J

source_name: SM/J

tag: SM/J


title: NOD/LtJ

description: epididymal fat was taken from 1 25-week old males and pooled

source_name: NOD/LtJ

tag: NOD/LtJ


title: PERA/EiJ

source_name: PERA/EiJ

tag: PERA/EiJ


title: DBA/2J


title: FVB/NJ

source_name: FVB/NJ

tag: FVB/NJ


title: SEA/GnJ

source_name: SEA/GnJ

tag: SEA/GnJ


title: RIIIS/J

source_name: RIIIS/J

tag: RIIIS/J


title: MOLF/EiJ

source_name: MOLF/EiJ

tag: MOLF/EiJ


title: NZW/LacJ

source_name: NZW/LacJ

tag: NZW/LacJ


title: MSM/Ms

source_name: MSM/Ms

tag: MSM/Ms


title: ovary 15

description: ovary

tag: tissue


title: PL/J

source_name: PL/J

tag: PL/J


title: C57L/J


title: NZB/BlNJ

source_name: NZB/BlNJ

tag: NZB/BlNJ


title: SJL/J

source_name: SJL/J

tag: SJL/J


title: cerebellum 3

description: cerebellum

source_name: cerebellum


title: JF1/Ms


title: C3H/HeJ

description: epididymal fat was taken from 4 25-week old males and pooled


title: CZECHII/EiJ

source_name: CZECHII/EiJ

tag: CZECHII/EiJ


title: BALB/cByJ

source_name: BALB/cByJ

tag: BALB/cByJ


title: A/J

source_name: A/J

tag: A/J


title: AKR/J

source_name: AKR/J

tag: AKR/J


title: uterus_4MJW061208169

status: Public on Apr 29 2008

description: uterus

source_name: uterus

label_protocol: For samples containing more than two µg total RNA available after pooling, standard Affymetrix single amplification was performed using two µg total RNA. For pooled samples containing less than two µg total RNA, 100 ng total RNA (or 50 ng for thymocyte_SP_CD8+) was used in a standard Affymetrix double amplification protocol.

extract_protocol: RNA extraction from mammalian cells or tissues was performed using RNeasy kits (Qiagen, Valencia, CA) or a standard Trizol protocol. If tissue amounts were more than 50 mg per mouse when dissected, tissues were pulverized while frozen. RNA was prepared separately for every mouse in order to identify samples with potentially degraded RNA. Trizol-extracted RNA was purified with a Qiagen RNeasy column. For bone marrow macrophages, osteoblasts, and osteoclasts, contaminating genomic DNA was removed during the RNeasy cleanup using DNaseI (Qiagen, Valencia, CA). The integrity and concentration of RNA was determined via microfluidic analysis on a bio-analyser (Agilent Technologies, Palo Alto, CA) or by analysis on a BioRad Experion. Pooling occurred at the RNA level.

treatment_protocol: All cell lines and tissues were sourced from 8-10 week old male C57Bl/6 mice, with the exception of female-specific organs, which were sourced from female mice. All procedures were carried out in accordance with local guidelines for animal research. For female tissues, material was pooled from three females, and for each female, on average four embryos resulting in four umbilical cords and placentas were obtained. For other tissues, material was derived from a pool of three males. Biological replicates were defined as independent RNA preparations from independent pools of mice. Technical replicates were defined as independent amplifications from the sample RNA sample.

tag: uterus


title: C57BL/6J


title: CBA/J

source_name: CBA/J

tag: CBA/J


title: BUB/BnJ

source_name: BUB/BnJ

tag: BUB/BnJ


title: umbilical_cord_4MJW061208185


title: BTBR_T+_tf/J


title: CAST/EiJ

source_name: CAST/EiJ

tag: CAST/EiJ


title: thymocyte_SP_CD4+_4MJW061208173


title: thymocyte_DP_CD4+CD8+_4MJW061208171


title: umbilical_cord_4MJW061208186


title: thymocyte_SP_CD8+_4MJW061208176


title: T-cells_CD4+_4MJW061208114


title: uterus_4MJW061208170

description: uterus


title: stomach_4MJW061208164

description: stomach

source_name: stomach

tag: stomach


title: testis_4MJW061208166

description: testis

source_name: testis

tag: testis


title: testis_4MJW061208165

description: testis


title: spleen_4MJW061208162

description: spleen

source_name: spleen

tag: spleen


title: spinal_cord_4MJW061208159


title: salivary_gland_4MJW061208182


title: thymocyte_SP_CD4+_4MJW061208174


title: T-cells_CD8+_4MJW061208116


title: stem_cells__HSC_4MJW06120877


title: thymocyte_SP_CD8+_4MJW061208175


title: T-cells_foxP3+_4MJW06120892


title: spleen_4MJW061208161

description: spleen


title: stomach_4MJW061208163

description: stomach


title: T-cells_CD8+_4MJW061208115


title: stem_cells__HSC_4MJW06120878


title: thymocyte_DP_CD4+CD8+_4MJW061208172


title: salivary_gland_4MJW061208181


title: T-cells_CD4+_4MJW061208113


title: T-cells_foxP3+_4MJW06120891


title: retinal_pigment_epithelium_4MJW06120893


title: RAW_264_7_4MJW06120838


title: RAW_264_7_4MJW06120837


title: spinal_cord_4MJW061208160


title: retina_4MJW06120895

description: retina

source_name: retina

tag: retina


title: retinal_pigment_epithelium_4MJW06120894


title: skeletal_muscle_4MJW061208156


title: skeletal_muscle_4MJW061208155


title: pituitary_4MJW061208151

description: pituitary

source_name: pituitary

tag: pituitary


title: placenta_4MJW061208189

description: placenta

source_name: placenta

tag: placenta


title: nucleus_accumbens_4MJW061208145


title: pancreas_4MJW06120813

description: pancreas

source_name: pancreas

tag: pancreas


title: placenta_4MJW061208190

description: placenta


title: prostate_4MJW061208154

description: prostate

source_name: prostate

tag: prostate


title: retina_4MJW06120896

description: retina


title: pancreas_4MJW06120814

description: pancreas


title: osteoblast_day14_4MJW06120865


title: pituitary_4MJW061208152

description: pituitary


title: osteoblast_day5_4MJW06120864


title: NK_cells_4MJW06120882


title: ovary_4MJW061208150

description: ovary

source_name: ovary

tag: ovary


title: olfactory_bulb_4MJW061208147


title: osteoblast_day14_4MJW06120866


title: olfactory_bulb_4MJW061208148


title: prostate_4MJW061208153

description: prostate


title: nih_3T3_4MJW06120836


title: osteoblast_day5_4MJW06120863


title: osteoclasts_4MJW06120862

description: osteoclasts

source_name: osteoclasts

tag: osteoclasts


title: osteoclasts_4MJW06120861

description: osteoclasts


title: osteoblast_day21_4MJW06120867


title: ovary_4MJW061208149

description: ovary


title: osteoblast_day21_4MJW06120868


title: nucleus_accumbens_4MJW061208146


title: mast_cells_IgE+antigen_1hr_4MJW06120886


title: mIMCD-3_4MJW06120832


title: min6_4MJW06120829


title: NK_cells_4MJW06120881


title: neuro2a_4MJW06120834


title: mast_cells_IgE+antigen_6hr_4MJW06120887


title: mast_cells_4MJW06120851


title: mast_cells_IgE_4MJW06120883


title: nih_3T3_4MJW06120835


title: mega_erythrocyte_progenitor_4MJW06120880


title: mammary_gland_non-lactating_4MJW061208144


title: neuro2a_4MJW06120833


title: mIMCD-3_4MJW06120831


title: microglia_4MJW061208183

description: microglia

source_name: microglia

tag: microglia


title: macrophage_peri_LPS_thio_7hrs_4MJW06120847


title: mast_cells_4MJW06120852


title: mast_cells_IgE+antigen_6hr_4MJW06120888


title: microglia_4MJW061208184

description: microglia


title: mast_cells_IgE_4MJW06120884


title: min6_4MJW06120830


title: mast_cells_IgE+antigen_1hr_4MJW06120885


title: mega_erythrocyte_progenitor_4MJW06120879


title: macrophage_peri_LPS_thio_1hrs_4MJW06120846


title: mammary_gland__lact_4MJW061208187


title: mammary_gland__lact_4MJW061208188


title: macrophage_peri_LPS_thio_7hrs_4MJW06120848


title: macrophage_bone_marrow_6hr_LPS_4MJW06120857


title: macrophage_peri_LPS_thio_0hrs_4MJW06120844


title: macrophage_bone_marrow_24h_LPS_4MJW06120859


title: macrophage_bone_marrow_0hr_4MJW06120854


title: lymph_nodes_4MJW06120840


title: macrophage_peri_LPS_thio_1hrs_4MJW06120845


title: macrophage_peri_LPS_thio_0hrs_4MJW06120843


title: liver_4MJW061208140

description: liver

source_name: liver

tag: liver


title: lung_4MJW061208141

description: lung

source_name: lung

tag: lung


title: lens_4MJW061208102

description: lens

source_name: lens

tag: lens


title: mammary_gland_non-lactating_4MJW061208143


title: lacrimal_gland_4MJW061208180


title: macrophage_bone_marrow_2hr_LPS_4MJW06120855


title: macrophage_bone_marrow_2hr_LPS_4MJW06120856


title: intestine_small_4MJW061208158


title: lung_4MJW061208142

description: lung


title: macrophage_bone_marrow_24h_LPS_4MJW06120860


title: iris_4MJW061208105

description: iris

source_name: iris

tag: iris


title: macrophage_bone_marrow_6hr_LPS_4MJW06120858


title: liver_4MJW061208139

description: liver


title: macrophage_bone_marrow_0hr_4MJW06120853


title: iris_4MJW061208106

description: iris


title: lymph_nodes_4MJW06120839


title: intestine_small_4MJW061208157


title: intestine_large_4MJW061208138


title: lens_4MJW061208101

description: lens


title: kidney_4MJW061208136

description: kidney

source_name: kidney

tag: kidney


title: kidney_4MJW061208135

description: kidney


title: hypothalamus_4MJW061208133

description: hypothalamus

source_name: hypothalamus

tag: hypothalamus


title: hippocampus_4MJW06120801

description: hippocampus

source_name: hippocampus

tag: hippocampus


title: lacrimal_gland_4MJW061208179


title: hippocampus_4MJW06120802

description: hippocampus


title: hypothalamus_4MJW061208134

description: hypothalamus


title: intestine_large_4MJW061208137


title: heart_4MJW061208132

description: heart

source_name: heart

tag: heart


title: heart_4MJW061208131

description: heart


title: granulocytes_mac1+gr1+_4MJW06120869


title: granulocytes_mac1+gr1+_4MJW06120870


title: eyecup_4MJW061208104

description: eyecup

source_name: eyecup

tag: eyecup


title: eyecup_4MJW061208103

description: eyecup


title: follicular_B-cells_4MJW06120849


title: granulo_mono_progenitor_4MJW06120876


title: follicular_B-cells_4MJW06120850


title: embryonic_stem_line_Bruce4_p13_4MJW06120818


title: epidermis_4MJW06120810

description: epidermis

source_name: epidermis

tag: epidermis


title: epidermis_4MJW06120809

description: epidermis


title: embryonic_stem_line_V26_2_p16_4MJW06120819


title: embryonic_stem_line_Bruce4_p13_4MJW06120817


title: dorsal_root_ganglia_4MJW061208128


title: granulo_mono_progenitor_4MJW06120875


title: dendritic_plasmacytoid_B220+_4MJW061208110


title: dorsal_root_ganglia_4MJW061208127


title: dorsal_striatum_4MJW061208129


title: dorsal_striatum_4MJW061208130


title: dendritic_cells_myeloid_CD8a-_4MJW061208111


title: cornea_4MJW06120899

description: cornea

source_name: cornea

tag: cornea


title: ciliary_bodies_4MJW06120897


title: cerebral_cortex_prefrontal_4MJW061208178


title: cerebral_cortex_4MJW061208126


title: common_myeloid_progenitor_4MJW06120873


title: cornea_4MJW061208100

description: cornea


title: dendritic_plasmacytoid_B220+_4MJW061208109


title: embryonic_stem_line_V26_2_p16_4MJW06120820


title: cerebral_cortex_prefrontal_4MJW061208177


title: ciliary_bodies_4MJW06120898


title: dendritic_cells_myeloid_CD8a-_4MJW061208112


title: C3H_10T1_2_4MJW06120828


title: C2C12_4MJW06120825


title: cerebellum_4MJW061208123

description: cerebellum

source_name: cerebellum

tag: cerebellum


title: dendritic_cells_lymphoid_CD8a+_4MJW061208107


title: C2C12_4MJW06120826


title: B-cells_marginal_zone_4MJW06120890


title: dendritic_cells_lymphoid_CD8a+_4MJW061208108


title: cerebral_cortex_4MJW061208125


title: bladder_4MJW061208122

description: bladder

source_name: bladder

tag: bladder


title: bladder_4MJW061208121

description: bladder


title: bone_marrow_4MJW06120841


title: C3H_10T1_2_4MJW06120827


title: bone_marrow_4MJW06120842


title: bone_4MJW06120812

description: bone

source_name: bone

tag: bone


title: Baf3_4MJW06120824


title: B-cells_marginal_zone_4MJW06120889


title: bone_4MJW06120811

description: bone


title: common_myeloid_progenitor_4MJW06120874


title: cerebellum_4MJW061208124

description: cerebellum


title: amygdala_4MJW061208120

description: amygdala

source_name: amygdala

tag: amygdala


title: 9B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

status: Public on Dec 10 2007

description: breast tumor biopsy

hyb_protocol: standard Affymetrix procedures except for use of a custom 24-channel fluidics machine and GCS2500 scanner


title: 3T3-L1_4MJW06120821


title: adrenal_gland_4MJW061208117


title: adrenal_gland_4MJW061208118


title: Baf3_4MJW06120823


title: 8A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 8A;pretreatment;female;breast tumor

tag: 8A;pretreatment;female;breast tumor


title: adipose_brown_4MJW06120815


title: 69B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 7A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 7A;pretreatment;female;breast tumor

tag: 7A;pretreatment;female;breast tumor


title: 8B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 9A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 9A;pretreatment;female;breast tumor

tag: 9A;pretreatment;female;breast tumor


title: 3T3-L1_4MJW06120822


title: 7B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 65B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 69A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 69A;pretreatment;female;breast tumor

tag: 69A;pretreatment;female;breast tumor


title: amygdala_4MJW061208119

description: amygdala


title: adipose_white_4MJW06120804


title: adipose_brown_4MJW06120816


title: adipose_white_4MJW06120803


title: 68A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 68A;pretreatment;female;breast tumor

tag: 68A;pretreatment;female;breast tumor


title: 64B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 63B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 65A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 65A;pretreatment;female;breast tumor

tag: 65A;pretreatment;female;breast tumor


title: 60B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 68B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 63A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 63A;pretreatment;female;breast tumor

tag: 63A;pretreatment;female;breast tumor


title: 64A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 64A;pretreatment;female;breast tumor

tag: 64A;pretreatment;female;breast tumor


title: 60A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 60A;pretreatment;female;breast tumor

tag: 60A;pretreatment;female;breast tumor


title: 5B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 5A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 5A;pretreatment;female;breast tumor

tag: 5A;pretreatment;female;breast tumor


title: 58A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 58A;pretreatment;female;breast tumor

tag: 58A;pretreatment;female;breast tumor


title: 57B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 57A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 57A;pretreatment;female;breast tumor

tag: 57A;pretreatment;female;breast tumor


title: 55B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 56A;pretreatment;female;breast tumor; not assessable

description: breast tumor biopsy

source_name: 56A;pretreatment;female;breast tumor

tag: 56A;pretreatment;female;breast tumor


title: 56B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

description: breast tumor biopsy


title: 58B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 51A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 51A;pretreatment;female;breast tumor

tag: 51A;pretreatment;female;breast tumor


title: 53A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 53A;pretreatment;female;breast tumor

tag: 53A;pretreatment;female;breast tumor


title: 59B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 4B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; not assessable

description: breast tumor biopsy


title: 51B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; responder

description: breast tumor biopsy


title: 52B;female;breast tumor;Letrozole, 2.5mg/day,oral, 10-14 days; nonresponder

description: breast tumor biopsy


title: 52A;pretreatment;female;breast tumor; nonresponder

description: breast tumor biopsy

source_name: 52A;pretreatment;female;breast tumor

tag: 52A;pretreatment;female;breast tumor


title: 50A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 50A;pretreatment;female;breast tumor

tag: 50A;pretreatment;female;breast tumor


title: 55A;pretreatment;female;breast tumor; responder

description: breast tumor biopsy

source_name: 55A;pretreatment;female;breast tumor

tag: 55A;pretreatment;female;breast tumor