title: 0.12mg/mL PZA:pH5.6 (4h) ( mAdb expid=24119 )

description:
H37Rv attB::pAIam (log-phase) was diluted to an OD of 0.05 in 7H9-based medium at pH5.6 +/- 0.12mg/mL PZA. RNA isolated from cultures after 4h at 37C.
array_print_batch : Mtaa-04
array_print_slide : 4_22
mAdb_expid : 24119
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 25ug/mL CPZ + 0.1mM GSNO: DMSO ( mAdb expid=50241 )

status: Public on Sep 01 2004

type: RNA

city: Rockville

first: Helena

middle: I

last: Boshoff

state: MD

address: 12441 Parklawn Drive

department: LIG

country: USA

institute: NIAID/ NIH

description:
H37Rv ATCC27294 was grown to an OD650 of 0.28. At this stage 50mL culture was treated with 50uL 25mg/mL CPZ in DMSO. After 3.5h 0.1mM (final) GSNO was added and RNA isolated after another 3h. Control culture was treated similarly with equivalent amounts of DMSO.
array_print_batch : Mtbb-03
array_print_slide : mtbb5-34
mAdb_expid : 50241
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

molecule: total RNA

organism: Mycobacterium tuberculosis H37Rv

source_name: CPZ/GSNO

source_name: DMSO


title: 10ug/mL menadione + 0.1mM GSNO: DMSO ( mAdb expid=50232 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50uL 10mg/mL menadione in DMSO whereas control culture was treated with equivalent amount of DMSO. 2.5 hours after menadione addition, GSNO was added to 0.1mM (from stock in DMSO) whereas control culture was treated with equivalent amount of DMSO.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-16
mAdb_expid : 50232
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: menadione/GSNO


title: 0.4mM NaN3: DMSO, 4h ( mAdb expid=50238 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50uL 0.4M NaN3 + 50uL DMSO whereas control culture was treated with equivalent amount of DMSO. RNA was isolated after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-24
mAdb_expid : 50238
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 5ug/mL Clofazimine + 0.1mM GSNO: DMSO ( mAdb expid=50237 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50uL 5mg/mL Clofazimine in DMSO. 2.5h after addition of CFZ, GSNO was added to final conc of 0.1mM and RNA was isolated after another 4h at 37C. Control culture for reference RNA was treated with equivalent amount of DMSO for 6.5h.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-23
mAdb_expid : 50237
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: CFZ + GSNO


title: 6ug/mL Menadione + 0.1mM GSNO: DMSO ( mAdb expid=50242 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.28. At this stage 50mL culture was treated with 50uL 6mg/mL menadione in DMSO. After 3.5h 0.1mM (final) GSNO was added and RNA isolated after another 3h. Control culture was treated similarly with equivalent amounts of DMSO.
array_print_batch : Mtbb-03
array_print_slide : mtbb5-35
mAdb_expid : 50242
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Menadione/GSNO


title: 25ug/mL CPZ: DMSO, 6h ( mAdb expid=50235 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50uL 25mg/mL CPZ in DMSO whereas control culture was treated with equivalent amount of DMSO. RNA was isolated after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-21
mAdb_expid : 50235
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: CPZ


title: 1.2mg/mL PZA:pH5.6 (4h) ( mAdb expid=24116 )

description:
H37Rv attB::pAIam (log-phase) was diluted to an OD of 0.05 in 7H9-based medium at pH5.6 +/- 1.2mg/mL PZA. RNA isolated from cultures after 4h at 37C.
array_print_batch : Mtaa-03
array_print_slide : 3_21
mAdb_expid : 24116
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized

source_name: PZA

source_name: ctrl


title: 0.12mg/mL PZA:pH5.6 (4h) ( mAdb expid=24115 )

description:
H37Rv attB::pAIam (log-phase) was diluted to an OD of 0.05 in 7H9-based medium at pH5.6 +/- 0.12mg/mL PZA. RNA isolated from cultures after 4h at 37C.
array_print_batch : Mtaa-03
array_print_slide : 3_20
mAdb_expid : 24115
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 0.4mM NaN3: DMSO ( mAdb expid=50233 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50uL 0.4M sodium azide + 50uL DMSO whereas control culture was treated with equivalent amount of DMSO. RNA was isolated after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-17
mAdb_expid : 50233
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 4d Dubos NRP-1: Dubos aerobic log phase ( mAdb expid=50234 )

description:
H37Rv ATCC 27294 was grown to OD 0.3 in Dubos and then diluted to OD 0.05 in Dubos. 80mL cultures were set up in 120mL spinner flasks and tightly sealed. RNA was isolated after 4 days (OD was less than 0.2). Control culture for reference RNA was grown to OD 0.3 in Dubos medium under aerobic conditions
array_print_batch : Mtbb-03
array_print_slide : mtbb4-20
mAdb_expid : 50234
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Dubos NRP-1

source_name: Dubos aerobic


title: 0.1mM GSNO: DMSO, 4h ( mAdb expid=50236 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50uL 0.1M GSNO + 50uL DMSO whereas control culture was treated with equivalent amount of DMSO. RNA was isolated after 4h
array_print_batch : Mtbb-03
array_print_slide : mtbb4-22
mAdb_expid : 50236
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: GSNO


title: 0.12mg/mL PZA:pH5.6 (4h) ( mAdb expid=24117 )

description:
H37Rv attB::pAIam (log-phase) was diluted to an OD of 0.05 in 7H9-based medium at pH5.6 +/- 0.12mg/mL PZA. RNA isolated from cultures after 4h at 37C.
array_print_batch : Mtaa-03
array_print_slide : 3_31
mAdb_expid : 24117
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 25ug/mL CPZ: DMSO, 6h ( mAdb expid=50239 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.28. At this stage 50mL culture was treated with 50uL 25mg/mL CPZ in DMSO whereas control culture was treated with equivalent amount of DMSO. RNA was isolated after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb5-32
mAdb_expid : 50239
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 0.12mg/mL PZA:pH5.6 (2.5h) ( mAdb expid=24112 )

description:
H37Rv attB::pAIam (log-phase) was diluted to an OD of 0.05 in 7H9-based medium at pH5.6 +/- 0.12mg/mL PZA. RNA isolated from cultures after 2.5h at 37C.
array_print_batch : Mtaa-03
array_print_slide : 3_80
mAdb_expid : 24112
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 1.2mg/mL PZA:pH5.6 (2h) ( mAdb expid=24110 )

description:
H37Rv attB::pAIam (log-phase) was diluted to an OD of 0.05 in 7H9-based medium at pH5.6 +/- 1.2mg/mL PZA. RNA isolated from cultures after 2h at 37C.
array_print_batch : Mtaa-03
array_print_slide : 3_45
mAdb_expid : 24110
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 0.4mM NaN3: DMSO, 4h ( mAdb expid=50227 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50uL 0.4M NaN3 + 50uL DMSO whereas control culture was treated with equivalent amount of DMSO. RNA was isolated after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-11
mAdb_expid : 50227
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: PBS/Tween80/DMSO: DMSO, 6h ( mAdb expid=50229 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.25. At this stage 50mL culture was harvested and then resuspended in 50mL PBS/Tween 80 (0.05%)(PBS contained Ca2+ and Mg2+) + 50uL DMSO. RNA was isolated after 6h. Reference RNA isolated from culture in normal 7H9-based medium (OD 0.25) treated with equivalent amount of DMSO.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-14
mAdb_expid : 50229
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: PBS/Tw/DMSO


title: 25ug/mL CPZ+ 0.1mM GSNO: DMSO ( mAdb expid=50231 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50uL 25mg/mL CPZ in DMSO whereas control culture was treated with equivalent amount of DMSO. 2.5 hours after CPZ addition, GSNO was added to 0.1mM (from stock in DMSO) whereas control culture was treated with equivalent amount of DMSO.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-15
mAdb_expid : 50231
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 25ug/mL CPZ + 0.1mM GSNO: DMSO ctrl ( mAdb expid=50224 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50uL 25mg/mL CPZ in DMSO whereas control culture was treated with equivalent amount of DMSO. 2 hours after addition of CPZ, GSNO was added to 0.1mM (from stock in GSNO) whereas equivalent amount of DMSO was added to control culture.. RNA isolated after another 4h at 37C.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-9
mAdb_expid : 50224
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 5ug/mL Clofazimine + 0.1mM GSNO: DMSO ( mAdb expid=50226 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50uL 5mg/mL Clofazimine in DMSO + 0.1mM GSNO (final conc) whereas control culture was treated with equivalent amount of DMSO. RNA isolation after total of 6h treatment.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-10
mAdb_expid : 50226
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: CFZ/GSNO


title: 0.02mM GSNO: DMSO, 6h ( mAdb expid=50222 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50uL 0.02M GSNO + 50uL DMSO whereas control culture was treated with equivalent amount of DMSO. RNA was isolated after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-8
mAdb_expid : 50222
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 0.12mg/mL PZA:pH5.6 (2h) ( mAdb expid=24109 )

description:
H37Rv attB::pAIam (log-phase) was diluted to an OD of 0.05 in 7H9-based medium at pH5.6 +/- 0.12mg/mL PZA. RNA isolated from cultures after 2h at 37C.
array_print_batch : Mtaa-03
array_print_slide : 3_44
mAdb_expid : 24109
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 20ug/mL CPZ: DMSO, 6h ( mAdb expid=49338 )

description:
H37Rv was grown to an OD650 of 0.25 in Dubos medium. At this stage 40mL culture was treated with 20ug/mL CPZ (final conc) in a total added volume of 70uL DMSO whereas control culture was treated with equivalent amount of DMSO. Total treatment time was 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-20
mAdb_expid : 49338
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: CPZ (Dubos)


title: 4d 20mM nitrate in Dubos NRP-1: aerobic Dubos ( mAdb expid=50220 )

description:
H37Rv ATCC 27294 was grown to OD 0.3 in Dubos and then diluted to OD 0.05 in Dubos containing 20mM KNO3. 80mL cultures were set up in 120mL spinner flasks and tightly sealed. RNA was isolated after 4 days (OD was less than 0.2). Control culture for reference RNA was grown to OD 0.3 in Dubos medium under aerobic conditions.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-6
mAdb_expid : 50220
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Dubos NRP-1/NO3


title: 60mJ/cm2 UV:ctrl (6h) ( mAdb expid=24094 )

description:
H37Rv at OD 0.3-0.4 harvested from 200mL, resuspended in 6mL medium, irradiated at 60mJ/cm2, resuspended in 200mL medium, returned to 37C and RNA isolated from 50mL at 6h. Reference RNA was from similarly treated but not irradiated cells.
array_print_batch : Mtaa-05
array_print_slide : 5_84
mAdb_expid : 24094
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized

source_name: UV


title: 10ug/mL menadione (Dubos): DMSO, 6h ( mAdb expid=49339 )

description:
H37Rv was grown to an OD650 of 0.25 in Dubos medium. At this stage 40mL culture was treated with 10ug/mL menadione in a total added volume of 70uL DMSO whereas control culture was treated with equivalent amount of DMSO. Total treatment time was 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-21
mAdb_expid : 49339
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: menadione


title: 0.1mM GSNO/20ug/mL CPZ: DMSO, 6h ( mAdb expid=49336 )

description:
H37Rv was grown to an OD650 of 0.25 in Dubos medium. At this stage 40mL culture was treated with 0.1mM GSNO and 20ug/mL CPZ (final conc) in a total added volume of 70uL DMSO whereas control culture was treated with equivalent amount of DMSO. Treatment time was 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-26
mAdb_expid : 49336
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: GSNO/CPZ


title: 25mJ/cm2 UV:ctrl (2h) ( mAdb expid=24089 )

description:
H37Rv at OD 0.3-0.4 harvested from 200mL, resuspended in 6mL medium, irradiated at 25mJ/cm2, resuspended in 200mL medium, returned to 37C and RNA isolated from 50mL at 2h. Reference RNA was from similarly treated but not irradiated cells.
array_print_batch : Mtaa-05
array_print_slide : 5_79
mAdb_expid : 24089
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 0.1mM GSNO/10ug/mL menadione: DMSO, 6h ( mAdb expid=49337 )

description:
H37Rv was grown to an OD650 of 0.25 in Dubos medium. At this stage 40mL culture was treated with 0.1mM GSNO and 10ug/mLmenadione in a total added volume of 70uL DMSO whereas control culture was treated with equivalent amount of DMSO. Total treatment time was 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-27
mAdb_expid : 49337
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: GSNO/menadione

source_name: DMSO


title: 4d Dubos NRP-1: Dubos aerobic log phase ( mAdb expid=50219 )

description:
H37Rv ATCC 27294 was grown to OD 0.3 in Dubos and then diluted to OD 0.05 in Dubos. 80mL cultures were set up in 120mL spinner flasks and tightly sealed. RNA was isolated after 4 days (OD was less than 0.2). Control culture for reference RNA was grown to OD 0.3 in Dubos medium under aerobic conditions.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-5
mAdb_expid : 50219
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: aerobic


title: 0.5uM Valinomycin: DMSO, 6h ( mAdb expid=49334 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 40mL culture was treated with 0.5uM Valinomycin (final conc) in a total added volume of 40uL DMSO whereas control culture was treated with equivalent amount of DMSO. RNA extraction after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-5
mAdb_expid : 49334
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Valinomycin


title: 50uM CCCP: DMSO, 6h ( mAdb expid=49332 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 40mL culture was treated with 50uM CCCP (from 50mM stock in DMSO) whereas control culture was treated with equivalent amount of DMSO. RNA isolated after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-2
mAdb_expid : 49332
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: CCCP


title: 50uM Nigericin: DMSO, 6h ( mAdb expid=49333 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 40mL culture was treated with 50uM Nigericin(final conc) in a total added volume of 40uL DMSO whereas control culture was treated with equivalent amount of DMSO.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-3
mAdb_expid : 49333
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Nigericin


title: 0.5uM Valinomycin/ 70mM KCl: DMSO, 6h ( mAdb expid=49335 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 40mL culture was treated with 0.5uM Valinomycin + 70mM KCl (final conc) in a total added volume of 40uL DMSO whereas control culture was treated with equivalent amount of DMSO. Treatment time was 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-6
mAdb_expid : 49335
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 4mM H2O2:ctrl (4h) ( mAdb expid=24087 )

description:
H37Rv at OD 0.3 treated for 4h with 4mM H2O2. Reference RNA from untreated culture
array_print_batch : Mtaa-05
array_print_slide : 5_56
mAdb_expid : 24087
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized

source_name: ctrl


title: 60mJ/cm2 UV:ctrl (2h) ( mAdb expid=24090 )

description:
H37Rv at OD 0.3-0.4 harvested from 200mL, resuspended in 6mL medium, irradiated at 60mJ/cm2, resuspended in 200mL medium, returned to 37C and RNA isolated from 50mL at 2h. Reference RNA was from similarly treated but not irradiated cells.
array_print_batch : Mtaa-05
array_print_slide : 5_82
mAdb_expid : 24090
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: PBS/Tw/DMSO: 7H9, 6h ( mAdb expid=49327 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 40mL culture was harvested and resuspended in 40mL PBS/0.05% Tween 80/70uL DMSO (PBS contains Ca and Mg) whereas control culture was resuspended in 7H9-based medium. Treatment time was 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-33
mAdb_expid : 49327
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 0.1mM GSNO/10ug/mL menadione: DMSO, 6h ( mAdb expid=49331 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 40mL culture was treated with 0.1mM GSNO and 10ug/mLmenadione in a total added volume of 70uL DMSO whereas control culture was treated with equivalent amount of DMSO. RNA extraction after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-30
mAdb_expid : 49331
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 25mJ/cm2 UV: ctrl (6h) ( mAdb expid=24093 )

description:
H37Rv at OD 0.3-0.4 harvested from 200mL, resuspended in 6mL medium, irradiated at 25mJ/cm2, resuspended in 200mL medium, returned to 37C and RNA isolated from 50mL at 6h. Reference RNA was from similarly treated but not irradiated cells.
array_print_batch : Mtaa-05
array_print_slide : 5_81
mAdb_expid : 24093
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 20ug/mL CPZ: DMSO, 6h ( mAdb expid=49326 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 40mL culture was treated with 20ug/mL CPZ (final conc) in a total added volume of 70uL DMSO whereas control culture was treated with equivalent amount of DMSO. Total treatment time was 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-31
mAdb_expid : 49326
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: CPZ


title: 4mM H2O2:ctrl (4h) ( mAdb expid=24088 )

description:
H37Rv at OD 0.3 treated for 4h with 4mM H2O2. Reference RNA from untreated culture
array_print_batch : Mtaa-05
array_print_slide : 5_66
mAdb_expid : 24088
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 1uM Valinomycin: DMSO, 6h ( mAdb expid=49269 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 1uM Valinomycin (stock in DMSO) whereas control culture was treated with an equivalent amount of DMSO. RNA extracted after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-75
mAdb_expid : 49269
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 0.1mM GSNO/20ug/mL CPZ: DMSO, 6h ( mAdb expid=49330 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 40mL culture was treated with 0.1mM GSNO (stock in DMSO)and 20ug/mL CPZ (final conc) in a total added volume of 70uL DMSO whereas control culture was treated with equivalent amount of DMSO. Total treatment time was 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-29
mAdb_expid : 49330
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 10ug/mL menadione: DMSO, 6h ( mAdb expid=49328 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 40mL culture was treated with 10ug/mL menadione in a total added volume of 70uL DMSO whereas control culture was treated with equivalent amount of DMSO. Treatment time was 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-32
mAdb_expid : 49328
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 4mM H2O2:ctrl (2h) ( mAdb expid=24084 )

description:
H37Rv at OD 0.3 treated for 2h with 4mM H2O2. Reference RNA from untreated culture
array_print_batch : Mtaa-05
array_print_slide : 5_26
mAdb_expid : 24084
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 4mM H2O2:ctrl (2h) ( mAdb expid=24083 )

description:
H37Rv at OD 0.3 treated for 2h with 4mM H2O2. Reference RNA from untreated culture
array_print_batch : Mtaa-04
array_print_slide : 4_28
mAdb_expid : 24083
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 4mM H2O2:ctrl (4h) ( mAdb expid=24085 )

description:
H37Rv at OD 0.3 treated for 4h with 4mM H2O2. Reference RNA from untreated culture
array_print_batch : Mtaa-03
array_print_slide : 3_61
mAdb_expid : 24085
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 50uM Nigericin: DMSO, 6h ( mAdb expid=49265 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50uM Nigericin (50mM stock in DMSO) whereas control culture was treated with an equivalent amount of DMSO. RNA extracted after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-10
mAdb_expid : 49265
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 4mM H2O2:ctrl (4h) ( mAdb expid=24086 )

description:
H37Rv at OD 0.3 treated for 4h with 4mM H2O2. Reference RNA from untreated culture
array_print_batch : Mtaa-05
array_print_slide : 5_24
mAdb_expid : 24086
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 2mM DTNB: DMSO ( mAdb expid=49263 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 2mM DTNB (from 2M stock in DMSO )whereas control culture was treated with an equivalent amount of DMSO. RNA extracted after 6h
array_print_batch : Mtbb-03
array_print_slide : mtbb3-7
mAdb_expid : 49263
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: DTNB


title: 4mM H2O2:ctrl (2h) ( mAdb expid=24082 )

description:
H37Rv at OD 0.3 treated for 2h with 4mM H2O2. Reference RNA from untreated culture
array_print_batch : Mtaa-04
array_print_slide : 4_25
mAdb_expid : 24082
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 50ug/mL Verapamil: DMSO, 6h ( mAdb expid=49267 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50ug/mL Verapamil (from 50mg/mL stock in DMSO) whereas control culture was treated with an equivalent amount of DMSO. RNA extracted after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-12
mAdb_expid : 49267
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Verapamil


title: 4mM H2O2:ctrl (2h) ( mAdb expid=24081 )

description:
H37Rv at OD 0.3 treated for 2h with 4mM H2O2. Reference RNA from untreated culture
array_print_batch : Mtaa-03
array_print_slide : 3_57
mAdb_expid : 24081
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 1uM Valinomycin: DMSO, 6h ( mAdb expid=49266 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 1uM Valinomycin (Stock in DMSO) whereas control culture was treated with an equivalent amount of DMSO. RNA extracted after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-11
mAdb_expid : 49266
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 1uM Valinomycin: DMSO, 6h ( mAdb expid=49139 )

description:
H37Rv was grown to an OD650 of 0.22. At this stage 50mL culture was treated with for 6h 1uM Valinomycin (5uL from 10mM stock in DMSO) + 45uL DMSO whereas control culture was treated with equivalent amount of DMSO
array_print_batch : Mtbb-03
array_print_slide : mtbb3-46
mAdb_expid : 49139
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 10uM Valinomycin: DMSO, 6h ( mAdb expid=49140 )

description:
H37Rv was grown to an OD650 of 0.22. At this stage 50mL culture was treated with for 6h 10uM Valinomycin (from 10mM stock in DMSO) whereas control culture was treated with equivalent amount of DMSO
array_print_batch : Mtbb-03
array_print_slide : mtbb3-47
mAdb_expid : 49140
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 2mM b-mercaptoethanol: DMSO, 6h ( mAdb expid=49262 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 2mM beta-mercaptoethanol + 50uL DMSO whereas control culture was treated with an equivalent amount of DMSO. RNA extracted after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-6
mAdb_expid : 49262
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: mercaptoethanol


title: 2mM DTT: DMSO, 6h ( mAdb expid=49138 )

description:
H37Rv was grown to an OD650 of 0.22. At this stage 50mL culture was treated with for 6h 2mM DTT (from 1M stock in water) + 50uL DMSO whereas control culture was treated with equivalent amount of DMSO
array_print_batch : Mtbb-03
array_print_slide : mtbb3-45
mAdb_expid : 49138
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: DTT


title: 4mM H2O2:ctrl (1h) ( mAdb expid=24080 )

description:
H37Rv at OD 0.3 treated for 1h with 4mM H2O2. Reference RNA from untreated culture
array_print_batch : Mtaa-03
array_print_slide : 3_56
mAdb_expid : 24080
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: Dubos NRP-1: Dubos log-phase ( mAdb expid=48964 )

description:
H37Rv was grown to an OD650 of 0.2 in Dubos based medium. RNA was isolated for control culture at this stage. Some of this culture was diluted to an OD650 of 0.006 and 17mL dispensed into Wayne style tubes (HSR 0.5). RNA isolated after 5 days.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-64
mAdb_expid : 48964
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: log-phase


title: 0.2ug/mL Mtm:ctrl (6h) ( mAdb expid=24079 )

description:
H37Rv at OD 0.3 treated for 6h with 0.2 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-05
array_print_slide : 5_58
mAdb_expid : 24079
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized

source_name: Mtm


title: 1mM DTNB: DMSO, 6h ( mAdb expid=49137 )

description:
H37Rv was grown to an OD650 of 0.22. At this stage 50mL culture was treated with for 6h 1mM DTNB (from 1M stock in DMSO) whereas control culture was treated with equivalent amount of DMSO
array_print_batch : Mtbb-03
array_print_slide : mtbb3-44
mAdb_expid : 49137
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 0.1mM GSNO/5ug/mL KCN: DMSO, 6h ( mAdb expid=48963 )

description:
H37Rv was grown to an OD650 of 0.2 in normal 7H9-based medium (+Tween80) before treating with 0.1mM GSNO (stock in DMSO) +5ug/mL KCN or equivalent amount of DMSO.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-43
mAdb_expid : 48963
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: GSNO/KCN


title: 0.2ug/mL Mtm:ctrl (4h) ( mAdb expid=24077 )

description:
H37Rv at OD 0.3 treated for 4h with 0.2 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-05
array_print_slide : 5_25
mAdb_expid : 24077
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 2mM DTT: DMSO, 6h ( mAdb expid=49264 )

description:
H37Rv was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 2mM DTT + 50uL DMSO whereas control culture was treated with an equivalent amount of DMSO. RNA extracted after 6h
array_print_batch : Mtbb-03
array_print_slide : mtbb3-8
mAdb_expid : 49264
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 10ug/mL methoxatin: DMSO, 6h ( mAdb expid=48961 )

description:
H37Rv was grown to an OD650 of 0.2 in normal 7H9-based medium (+Tween) before treatment for 6h with 50uL 10mg/mL methoxatin / DMSO per 50mL culture or equivalent amount of DMSO
array_print_batch : Mtbb-03
array_print_slide : mtbb3-40
mAdb_expid : 48961
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: methoxatin


title: 0.1mM GSNO: DMSO, 6h ( mAdb expid=48962 )

description:
H37Rv was grown in normal 7H9-based medium to an OD650 of 0.2. At this stage 50mL culture was treated at 0.1mM GNSO (stock in DMSO) or equivalent amount of DMSO for 6h
array_print_batch : Mtbb-03
array_print_slide : mtbb3-42
mAdb_expid : 48962
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: GSNO


title: 0.2ug/mL Mtm:ctrl (4h) ( mAdb expid=24078 )

description:
H37Rv at OD 0.3 treated for 4h with 0.2 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-05
array_print_slide : 5_67
mAdb_expid : 24078
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 7d Dubos NRP-1: Dubos log phase ( mAdb expid=48958 )

description:
H37Rv was grown in Dubos based medium to an OD of 0.2 before diluted to an OD650 of 0.006 and 17mL dispensed into Wayne-style closed cap tubes (HSR 0.5). RNA was isolated after 7 days in these tubes (NRP-1) whereas control RNA was obtained from log-phase culture culture (OD 0.3) in Dubos.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-62
mAdb_expid : 48958
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: log


title: 0.2ug/mL Mtm:ctrl (4h) ( mAdb expid=24076 )

description:
H37Rv at OD 0.3 treated for 4h with 0.2 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-03
array_print_slide : 3_10
mAdb_expid : 24076
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 20ug/mL methoxatin: DMSO, 6h ( mAdb expid=48960 )

description:
H37Rv was grown in normal 7H9-based medium (with Tween) to an OD650 of 0.2 before treatment for 6h with 20ug/mL methoxatin (from 10mg/mL stock) or 50uL DMSO/50mL culture for reference RNA extraction.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-41
mAdb_expid : 48960
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: DMSO


title: 7d Dubos NRP-1: Dubos log phase ( mAdb expid=48957 )

description:
H37Rv was grown in Dubos based medium to an OD of 0.2 before diluted to an OD650 of 0.006 and 17mL dispensed into Wayne-style closed cap tubes (HSR 0.5). RNA was isolated after 7 days in these tubes (NRP-1) whereas control RNA was obtained from log-phase culture culture (OD 0.3) in Dubos.
array_print_batch : Mtbb-03
array_print_slide : mtbb3-63
mAdb_expid : 48957
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 0.1mM GSNO: DMSO, 6h ( mAdb expid=48956 )

description:
H37Rv was grown to an OD650 of 0.2 in 7H9-based medium without Tween (there was no clumping since Tween was only omitted at end) and then treated at 0.1mM GSNO (stock in DMSO) + 5ug/mL KCN (stock in water for 6h before RNA extraction
array_print_batch : Mtbb-03
array_print_slide : mtbb3-60
mAdb_expid : 48956
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 0.2ug/mL Mtm:ctrl (4h) ( mAdb expid=24075 )

description:
H37Rv at OD 0.3 treated for 4h with 0.2 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-04
array_print_slide : 4_71
mAdb_expid : 24075
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 0.2ug/mL Mtm:ctrl (4h) ( mAdb expid=24074 )

description:
H37Rv at OD 0.3 treated for 4h with 0.2 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-03
array_print_slide : 3_62
mAdb_expid : 24074
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 0.1mM GSNO/5ug/mL KCN: DMSO, 6h ( mAdb expid=48955 )

description:
H37Rv was grown to an OD650 of 0.2 in 7H9-based medium without Tween (there was no clumping since Tween was only omitted at end) and then treated at 0.1mM GSNO (stock in DMSO) + 5ug/mL KCN (stock in water for 6h before RNA extraction
array_print_batch : Mtbb-03
array_print_slide : mtbb3-61
mAdb_expid : 48955
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 10mM Succinate (min med): 10mM Glucose (min med) ( mAdb expid=48023 )

description:
H37Rv from a stationary phase culture in 7H9-based medium was washed twice in minimal medium without C-source. The cells were subsequently diluted into minimal medium containing either 10mM glucose or 10mM succinate and grown for 1 week until OD = 0.3 before extracting RNA
array_print_batch : Mtbb-02
array_print_slide : mtbb2-58
mAdb_expid : 48023
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: succinate

source_name: glucose


title: 1ug/mL ARP2: DMSO, 6h ( mAdb expid=48020 )

description:
H37Rv was grown to an OD650 of 0.2. 50mL of culture was treated for 6h with either 50uL 1mg/mL  compound ARP2 in DMSO or 50uL DMSO before RNA extraction
array_print_batch : Mtbb-02
array_print_slide : mtbb2-60
mAdb_expid : 48020
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 4ug/mL ARP2: DMSO, 6h ( mAdb expid=48022 )

description:
H37Rv was grown to an OD650 of 0.2. 50mL of culture was treated for 6h with either 50uL 4mg/mL  compound ARP2 in DMSO or 50uL DMSO before RNA extraction
array_print_batch : Mtbb-02
array_print_slide : mtbb2-61
mAdb_expid : 48022
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 0.2ug/mL Mtm:ctrl (2h) ( mAdb expid=24073 )

description:
H37Rv at OD 0.3 treated for 2h with 0.2 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-05
array_print_slide : 5_23
mAdb_expid : 24073
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 10ug/mL Methoxatin: DMSO, 6h ( mAdb expid=48954 )

description:
H37Rv was grown in 7H9-based medium without Tween 80 to an OD650 of 0.2 and then 50mL culture was treated with 50uL methoxatin in DMSO or DMSO alone for 6h before RNA extraction
array_print_batch : Mtbb-03
array_print_slide : mtbb3-59
mAdb_expid : 48954
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Methoxatin


title: 0.2ug/mL Mtm:ctrl (2h) ( mAdb expid=24070 )

description:
H37Rv at OD 0.3 treated for 2h with 0.2 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-03
array_print_slide : 3_58
mAdb_expid : 24070
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: SynovChrAr_022LACIF_152.txt

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

institute: Cincinnati Children's Hospital Medical Center

description:
Synovium; chronic arthritis
Keywords = mouse gene expression database

organism: Mus musculus

source_name: Universal mouse reference RNA


title: 0.2ug/mL Mtm:ctrl (2h) ( mAdb expid=24072 )

description:
H37Rv at OD 0.3 treated for 2h with 0.2 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-04
array_print_slide : 4_29
mAdb_expid : 24072
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized

source_name: ctrl


title: 0.2ug/mL Mtm:ctrl (2h) ( mAdb expid=24071 )

description:
H37Rv at OD 0.3 treated for 2h with 0.2 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-04
array_print_slide : 4_27
mAdb_expid : 24071
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: SynovChrAr_022OACJ1_152.txt


title: 4ug/mL ARP4: DMSO, 6h ( mAdb expid=48019 )

description:
H37Rv was grown to an OD650 of 0.2. 50mL of culture was treated for 6h with either 50uL 4mg/mL  compound ARP4 in DMSO or 50uL DMSO before RNA extraction
array_print_batch : Mtbb-02
array_print_slide : mtbb2-87
mAdb_expid : 48019
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 0.2ug/mL Mtm:ctrl (1.5h) ( mAdb expid=24069 )

description:
H37Rv at OD 0.3 treated for 1.5h with 0.2 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-03
array_print_slide : 3_18
mAdb_expid : 24069
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 0.05mM Palmitate (min med): 10mM Glucose (min med) ( mAdb expid=47906 )

description:
H37Rv had been grown to an OD of 0.4-0.5 in defined minimal medium contaning respective C-source (glucose or palmitate). A dilution was made of this culture into fresh minimal medium containing respective C-source (0.05mM palmitate or 10mM glucose) and grown for three more days until OD 0.3 before RNA isolation. Glucose cells = reference, palmitate = test.
array_print_batch : Mtbb-02
array_print_slide : mtbb2-45
mAdb_expid : 47906
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Palmitate

source_name: Glucose


title: 0.1ug/mL Mtm:ctrl (0.75h) ( mAdb expid=24067 )

description:
H37Rv at OD 0.3 treated for 0.75h with 0.1 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-03
array_print_slide : 3_13
mAdb_expid : 24067
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 0.2ug/mL Mtm:ctrl (0.75h) ( mAdb expid=24068 )

description:
H37Rv at OD 0.3 treated for 0.75h with 0.2 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-03
array_print_slide : 3_17
mAdb_expid : 24068
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: 25ug/mL CPZ: DMSO ctrl, 6h ( mAdb expid=50221 )

description:
H37Rv ATCC27294 was grown to an OD650 of 0.25. At this stage 50mL culture was treated with 50uL 25mg/mL CPZ in DMSO whereas control culture was treated with equivalent amount of DMSO. RNA was isolated after 6h.
array_print_batch : Mtbb-03
array_print_slide : mtbb4-7
mAdb_expid : 50221
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: CPZ


title: 10mM Succinate (min med): 10mM Glucose (min med) ( mAdb expid=47905 )

description:
H37Rv had been grown to an OD of 0.4-0.5 in defined minimal medium containing the respective C-source (10mM succinate or 10mM glucose). A dilution was made of this culture into fresh minimal medium containing respective C-source (10mM succinate or 10mM glucose) and grown for three more days until OD 0.3 before RNA isolation. Glucose cells = reference, succinate = test.
array_print_batch : Mtbb-02
array_print_slide : mtbb2-44
mAdb_expid : 47905
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: 10mM Succinate

source_name: 10mM Glucose


title: 1ug/mL ARP4: DMSO, 6h ( mAdb expid=48018 )

description:
H37Rv was grown to an OD650 of 0.2. 50mL of culture was treated for 6h with either 50uL 1mg/mL compound ARP4 in DMSO or 50uL DMSO before RNA extraction
array_print_batch : Mtbb-02
array_print_slide : mtbb2-86
mAdb_expid : 48018
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: SynovAcAr_022HACJ0_151.txt

description:
Synovium; acute arthritis
Keywords = mouse gene expression database


title: SynovAcAr_022EACIE_151.txt


title: 1mM DNP: DMSO, 6h ( mAdb expid=47899 )

description:
H37Rv was grown to an OD of 0.30 in normal 7H9-based medium. At this stage 50mL culture was treated with 50uL 1M dinitrophenol in DMSO or 50uL DMSO alone. RNA was isolated after 6h
array_print_batch : Mtbb-01
array_print_slide : mtbb1-43
mAdb_expid : 47899
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: DNP


title: 25ug/mL Thioridazine: DMSO, 6h ( mAdb expid=47900 )

description:
H37Rv was grown to an OD of 0.30 in normal 7H9-based medium. At this stage 50mL culture was treated with 50uL 25mg/mL thioridazine in DMSO or 50uL DMSO alone. RNA was isolated after 6h
array_print_batch : Mtbb-01
array_print_slide : mtbb1-44
mAdb_expid : 47900
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: TRZ


title: 0.05mM Palmitate (min med): 10mM Glucose (min med) ( mAdb expid=48024 )

description:
H37Rv from a stationary phase culture in 7H9-based medium was washed twice in minimal medium without C-source. The cells were subsequently diluted into minimal medium containing either 10mM glucose or 0.05mM palmitate and grown for 1 week until OD = 0.3 before extracting RNA
array_print_batch : Mtbb-02
array_print_slide : mtbb2-59
mAdb_expid : 48024
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: palmitate


title: 0.05mM Palmitate (min med): 10mM Glucose (min med) ( mAdb expid=47898 )

description:
H37Rv (mid-log in 7H9-based medium) was washed in defined minimal medium without carbon source. Cells were then diluted into defined minimal medium containing either 0.05mM palmitate or 10mM glucose (reference) as C-source and grown for four days until OD 0.3.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-42
mAdb_expid : 47898
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 0.2ug/mL Mtm:ctrl (0.33h) ( mAdb expid=24066 )

description:
H37Rv at OD 0.3 treated for 0.33h with 0.2 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-03
array_print_slide : 3_15
mAdb_expid : 24066
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized

source_name: Mtm


title: 0.1ug/mL Mtm:ctrl (0.33h) ( mAdb expid=24065 )

description:
H37Rv at OD 0.3 treated for 0.33h with 0.1 ug/mL Mitomycin C. Reference RNA from untreated culture
array_print_batch : Mtaa-03
array_print_slide : 3_12
mAdb_expid : 24065
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio, normalized


title: Stroma vascular fraction 3

city: Toulouse

first: Guillaume

last: Charriere

country: France

description:
primary SVF cells, 24h after plating. SVF cells were isolated with a collagenase based standard protocol. SVF cells were plated in DMEM-F12 + 10% NCS medium for 24h. Only adherent cells were used for the RNA extraction. RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, white adipose tissue, Stroma-vascular-fraction cells.

source_name: Inguinal white adipose tissue


title: 10ug/mL Novobiocin: DMSO, 6h ( mAdb expid=47901 )

description:
H37Rv was grown to an OD of 0.30 in normal 7H9-based medium. At this stage 50mL culture was treated with 50uL 10mg/mL Novobiocin in DMSO or 50uL DMSO alone. RNA was isolated after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-46
mAdb_expid : 47901
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Novobiocin


title: Stroma vascular fraction 2


title: LivReSham6h22EAFIH_181.txt

description:
Liver; RegenerationSham 6 hrs
Keywords = mouse gene expression database


title: 10mM Succinate (min med): 10mM Glucose (min med) ( mAdb expid=47897 )

description:
H37Rv (mid-log in 7H9-based medium) was washed in defined minimal medium without carbon source. Cells were then diluted into defined minimal medium containing either 10mM Succinate or 10mM glucose (reference) as C-source and grown for four days until OD 0.3.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-41
mAdb_expid : 47897
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Succinate


title: LivRegen6h_022LAFAU_063.txt

description:
Liver; Regeneration 6h
Keywords = mouse gene expression database


title: Stroma vascular fraction 1


title: 10ug/mL Thioridazine: DMSO, 6h ( mAdb expid=47896 )

description:
H37Rv was grown to an OD650 of 0.30. At this stage 50mL culture was treated with 50uL 10mg/mL TRZ/DMSO or 50uL DMSO for 6h before RNA isolation
array_print_batch : Mtbb-02
array_print_slide : mtbb2-47
mAdb_expid : 47896
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: DMSO


title: LivReSham6h22LAFII_181.txt


title: LivRegen24hr022SAFAV_180.txt

description:
Liver; Regeneration 24 hrs
Keywords = mouse gene expression database


title: LivRegen6hr_022JAC3D_063.txt


title: LivRegen24hr022CAC3C_180.txt


title: 10ug/mL Novobiocin: DMSO, 6h ( mAdb expid=47758 )

description:
H37Rv was grown to an OD650 of 0.30 in normal 7H9-based medium. At this stage 50mL culture was treated with 50uL 10mg/mL Novobiocin in DMSO whereas control culture was treated with 50uL DMSO. RNA was extracted after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-40
mAdb_expid : 47758
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: IWAT isolated Adipocytes #3

description:
Adipocytes were isolated with a collagenase based standard protocol. Adipocytes were washed twice in PBS. RNA extraction was performed with TRIPURE reagents and protocol, lipids were removed just after adipocytes lysis into Tripure solution. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, white adipose tissue, Adipocytes.


title: Differentiated 3T3-F442A day 7 #3

description:
3T3-F442A cells were cultered  to reach confluence. At confluence state, the cells were cultured in DMEM + 10% FCS medium with Rosiglitazone (thialozidinedione) for seven days. Differentiation was estimate on the number and size of lipid droplets content into the cells. RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, adipocyte,  3T3-F442A.

source_name: 3T3-F442A predipocyte cell line


title: IWAT isolated Adipocytes #2


title: IWAT isolated Adipocytes #1


title: 5ug/mL KCN: DMSO, 6h ( mAdb expid=47757 )

description:
H37Rv was grown to an OD650 of 0.30 in normal 7H9-based medium. At this stage 50mL culture was treated with 25uL 10mg/mL KCN in water + 50uL DMSO whereas control culture was treated with 50uL DMSO. RNA isolated after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-39
mAdb_expid : 47757
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: KCN


title: KidFA_022UACJ7_fa2.txt

description:
Kidney; FVB/N Folic Acid toxic injury
Keywords = mouse gene expression database

source_name: Universal mouse reference RNA


title: HeartHDmekt_022KAFIN_123t.txt

description:
Heart; tg - hyperdynamic
Keywords = mouse gene expression database


title: Differentiated 3T3-F442A day 7 #2


title: B-ALL-10

city: New York

first: Dong-Joon

last: Min

state: NY

institute: Mount Sinai School of Medicine

description: RNA extracted using Trizol. Double round amplification completed with Arcturus RiboAmp kit.

organism: Homo sapiens

source_name: Bone marrow sample


title: HeartHDmekt_022GACJ5_123t.txt


title: KidFA_022YAFIP_fa2.txt


title: B-ALL-9


title: Differentiated 3T3-F442A day 7 #1


title: B-ALL-8


title: Min med - Succinate: Min med glucose ( mAdb expid=47754 )

description:
H37Rv was grown for 2 days in minimal medium containing 0.05% Tween 80 and 10mM succinate as sole carbon source. OD650 at start was 0.157 and after 2d was 0.404. RNA was extracted and labeled with Cy5. Cy3 label used similarly grown culture except that C-source was 10mM glucose.
array_print_batch : Mtbb-02
array_print_slide : mtbb2-34
mAdb_expid : 47754
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Min med Succinate

source_name: Min med Glucose


title: HeartCtrlMek_022DAFBS_123w.txt

description:
Heart; HyperdynamicControl
Keywords = mouse gene expression database


title: Min med -Palmitate: Min med - Glucose ( mAdb expid=47753 )

description:
H37Rv was grown for 2 days in minimal medium containing 0.05% Tween 80 and 0.05mM Sodium palmitate as sole carbon source. OD650 at start was 0.20 and after 2d was 0.356. RNA was extracted and labeled with Cy5. Cy3 label used similarly grown culture except that C-source was 10mM glucose.
array_print_batch : Mtbb-02
array_print_slide : Mtbb2-35
mAdb_expid : 47753
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Min Med - Palmitate

source_name: Min med - Glucose


title: B-ALL-6


title: B-ALL-7


title: 50uM CCCP: DMSO, 6h ( mAdb expid=47751 )

description:
H37Rv was grown to an OD650 of 0.30. At this stage 50uL 50mM CCCP in DMSO was added to 50mL (the treated) culture, whereas 50uL DMSO was added to 50mL of control culture. RNA extracted after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-17
mAdb_expid : 47751
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: CCCP


title: 20uM DCCD: DMSO, 6h ( mAdb expid=47756 )

description:
H37Rv was grown to an OD650 of 0.30 in normal 7H9-based medium. At this stage 50mL culture was treated with 25uL 40mM DCCD in DMSO + 25uL DMSO whereas control culture was treated with 50uL DMSO. RNA isolated after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-38
mAdb_expid : 47756
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: DCCD


title: UterPreg45_022KACIK_111.txt

description:
Female; Uterus - pregnant day4.5
Keywords = mouse gene expression database


title: non-differentiated ESC #2

description:
ZIN40 were cultered in low density to avoid confluence state. The cells were cultured in GMEM + 10% FCS medium + LIF to maintain totipotence.  RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, Embryonic stem cell, ZIN40.

source_name: ZIN40 ES cell line


title: 50uM CCCP: DMSO, 6h ( mAdb expid=47755 )

description:
H37Rv was grown to an OD650 of 0.30 in normal 7H9-based medium. At this stage 50mL culture was treated with 50uL 50m CCCP in DMSO whereas control culture was treated with 50uL DMSO. RNA was extracted after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-36
mAdb_expid : 47755
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: HeartCtrlMek_0229ACJ4_123w.txt


title: B-ALL-5


title: B-ALL-4


title: non-differentiated ESC #1


title: differentiated ESC #3

description:
ZIN40 were cultered in low density to avoid confluence state. The cells were cultured for few passages in GMEM + 10% FCS medium without LIF to engaged them and making them lost their totipotency.  RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, Embryonic stem cell, ZIN40.


title: 20uM DCCD: DMSO, 6h ( mAdb expid=47750 )

description:
H37Rv was grown to an OD650 of 0.30. At this stage 25uL 40mM dicyclohexylcarboxydiimide in DMSO + 25uL DMSO was added to 50mL (the treated) culture, whereas 50uL DMSO was added to 50mL of control culture. RNA isolation after 6h.
array_print_batch : Mtbb-02
array_print_slide : mtbb2-18
mAdb_expid : 47750
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 0.5mM DNP: DMSO, 6h ( mAdb expid=47749 )

description:
H37Rv was grown to an OD650 of 0.30. At this stage 50uL 0.5M dinitrophenol in DMSO was added to 50mL (the treated) culture, whereas 50uL DMSO was added to 50mL of control culture. RNA extracted after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-19
mAdb_expid : 47749
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: DNP


title: #41 C1-3 vs 46J-2-5.txt

description:
Small Intestine; proximal jejunum 46
Keywords = mouse gene expression database

source_name: GI, Pjej46WT


title: UterPreg45_022CACHU_111.txt


title: B-ALL-3


title: #92 C1-3 vs 46J-5.txt


title: 5ug/mL KCN: DMSO, 6h ( mAdb expid=47748 )

description:
H37Rv was grown to an OD650 of 0.30. At this stage 25uL 10mg/mL KCN in water + 50uL DMSO was added to 50mL (the treated) culture, whereas 50uL DMSO was added to 50mL of control culture. RNA extracted after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-20
mAdb_expid : 47748
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: B-ALL-2


title: differentiated ESC #2


title: IleumSham_22XAFB7_176.txt

description:
Small Intestine; ileum sham short bowel resection
Keywords = mouse gene expression database

source_name: GI, ILSham


title: non-differentiated ESC #3


title: differentiated ESC #1


title: Liver samples #1

description:
Liver samples were isolated  mechanicaly. RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, liver tissue.

source_name: liver


title: IleumSham_022SAF6P_176.txt


title: Liver samples #2


title: J774 cells #2

description:
J774 were cultered in low density to avoid confluence state. The cells were cultured in DMEM + 10% FCS medium for few passages.  RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus,macrophage, J774.

source_name: J774 macrophage cell line


title: J774 cells #1


title: 10ug/mL Novobiocin: DMSO, 6h ( mAdb expid=47747 )

description:
H37Rv was grown to an OD650 of 0.30. At this stage 50uL 10mg/mL Novobiocin in DMSO was added to 50mL (the treated) culture, whereas 50uL DMSO was added to 50mL of control culture. RNA extracted after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-21
mAdb_expid : 47747
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Novobiocin

source_name: DMSO


title: 100ug/mL Cephalexin: DMSO, 6h ( mAdb expid=47745 )

description:
H37Rv was grown to an OD650 of 0.30. At this stage 500uL 10mg/mL Cephalexin + 50uL DMSO was added to 50mL (the treated) culture, whereas 50uL DMSO was added to 50mL of control culture. RNA extracted after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-23
mAdb_expid : 47745
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Ceph


title: 10ug/mL Thioridazine: DMSO, 6h ( mAdb expid=47746 )

description:
H37Rv was grown to an OD650 of 0.30. At this stage 50uL 10mg/mL Thioridazine in DMSO was added to 50mL (the treated) culture, whereas 50uL DMSO was added to 50mL of control culture. RNA extracted after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-41
mAdb_expid : 47746
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: TRZ


title: B-ALL-1

description: RNA extracted using Trizol. Double round amplification completed with Arcturus RiboAmp kit.

source_name: Bone marrow sample


title: 1mM DNP: DMSO, 6h ( mAdb expid=47453 )

description:
H37Rv was grown to an OD of 0.3 in normal 7H9-based medium. 50mL of culture was treated with 50uL of 1M dinitrophenol in DMSO whereas control culture was treated with 50uL DMSO. RNA was extracted after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-12
mAdb_expid : 47453
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 20ug/mL KCN: DMSO, 6h ( mAdb expid=47454 )

description:
H37Rv was grown to an OD of 0.3 in normal 7H9-based medium. 50mL of culture was treated with 50uL of 20mg/mL KCN (in water) + 50uL DMSO whereas control culture was treated with 50uL DMSO. RNA was extracted after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-13
mAdb_expid : 47454
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: KCN


title: #74 C1-3 vs 59J-5.txt

description:
GI_canc, Jejunal tumor 59
Keywords = mouse gene expression database

source_name: GI_canc, Jej59

source_name: Universal mouse reference RNA


title: #75 C1-3 vs 59J-2-5.txt

description:
GI_canc, Jejunal tumor j59
Keywords = mouse gene expression database


title: #06 C1-3 vs 48J-5.txt

description:
GI_canc, Jejunal tumor 48
Keywords = mouse gene expression database

source_name: GI_canc, Jej48


title: T-ALL-9


title: T-ALL-10


title: Raw 264 cells #3

description:
Raw 264 cells were cultered in low density to avoid confluence state. The cells were cultured in DMEM + 10% FCS medium for few passages.  RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, macrophage,  Raw 264.

source_name: Raw 264 macrophage cell line


title: #07 C1-3 vs 48J-2-5.txt

description:
GI_canc, Jejunal tumor j48
Keywords = mouse gene expression database


title: T-ALL-7


title: Raw 264 cells #2


title: Raw 264 cells #1


title: T-ALL-5


title: T-ALL-8


title: JejunTum2_022IAFCX_J1.txt

description:
Cancers; Prox.Jejunum tumor
Keywords = mouse gene expression database

source_name: GI_canc, Jej3


title: C3H-10T1/2 cells in proliferation #3

description:
C3H-10T1/2 were cultered in low density to avoid confluence state. The cells were cultured in DMEM + 10% FCS medium for few passages.  RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, mesenchymal stem cell, C3H-10T1/2.

source_name: C3H-10T1/2 mesenchymal stem cell line


title: 100uM DCCD: DMSO, 6h ( mAdb expid=47452 )

description:
H37Rv was grown to an OD of 0.3 in normal 7H9-based medium. 50mL of culture was treated with 50uL of 100mM dicyclohexyl-carboxydiimide (drug in DMSO, fresh) whereas control culture was treated with 50uL DMSO
array_print_batch : Mtbb-02
array_print_slide : mtbb2-11
mAdb_expid : 47452
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: DCCD


title: T-ALL-6


title: 100ug/mL Cephalexin: DMSO, 6h ( mAdb expid=47451 )

description:
H37Rv was grown to an OD of 0.3 in normal 7H9-based medium. 50mL of culture was treated with 100ug/mL Cephalexin (drug in water) + 50uL DMSO whereas control culture was treated with 50uL DMSO. RNA was isolated after 6h
array_print_batch : Mtbb-02
array_print_slide : mtbb2-10
mAdb_expid : 47451
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Cephalexin


title: JejunTumorNew_0221AFCA_jtc.txt

source_name: GI_canc, Jej2


title: JejunTumorNew_0228AFCB_jtc.txt


title: C3H-10T1/2 cells in proliferation #2


title: C3H-10T1/2 cells in proliferation #1


title: T-ALL-3


title: 0.2ug/mL PA824: DMSO, 6h ( mAdb expid=45829 )

description:
H37Rv was grown to an OD of 0.3. At this stage 50mL culture was treated either with 50uL 0.2mg/mL PA824 in DMSO or DMSO alone. RNA was extracted from cultures after 6h.
array_print_batch : Mtbb-01
array_print_slide : mtbb2-1
mAdb_expid : 45829
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: JejuPrxTumor2022JAFBY_jtc.txt

source_name: GI_canc, Jej1


title: 10uM CCCP: DMSO, 6h ( mAdb expid=47431 )

description:
H37Rv was grown to an OD of 0.3 in normal 7H9-based medium. 50mL of culture was treated with 50uL of 10mM CCCP whereas control culture was treated with 50ul DMSO. RNA was extracted after 6h.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-40
mAdb_expid : 47431
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: CCCP


title: T-ALL-4


title: 0.4ug/mL PA824: DMSO, 6h ( mAdb expid=45828 )

description:
H37Rv was grown to an OD of 0.3. At this stage 50mL culture was treated either with 50uL 0.4mg/mL PA824 in DMSO or DMSO alone. RNA was extracted from cultures after 6h.
array_print_batch : Mtbb-01
array_print_slide : mtbb2-3
mAdb_expid : 45828
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 0.4ug/mL PA824: DMSO, 6h ( mAdb expid=45830 )

description:
H37Rv was grown to an OD of 0.3. At this stage 50mL culture was treated either with 50uL 0.4mg/mL PA824 in DMSO or DMSO alone. RNA was extracted from cultures after 6h.
array_print_batch : Mtbb-01
array_print_slide : mtbb2-4
mAdb_expid : 45830
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: Tibialis isolated muscle samples #2

description:
Muscle samples were isolated from tibialis mechanicaly. RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, muscle tissue.

source_name: muscle


title: 0.2ug/mL PA824: DMSO, 6h ( mAdb expid=45827 )

description:
H37Rv was grown to an OD of 0.3. At this stage 50mL culture was treated either with 50uL 0.2mg/mL PA824 in DMSO or DMSO alone. RNA was extracted from cultures after 6h.
array_print_batch : Mtbb-01
array_print_slide : mtbb2-2
mAdb_expid : 45827
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: DMSO


title: Tibialis isolated muscle samples #1


title: JejuPrxTumor1022CAFBX_jtc.txt


title: T-ALL-2

description: RNA extracted using Trizol. Double round amplification completed with Arcturus RiboAmp kit.


title: T-LL-9

source_name: Lymphoma tissue


title: #57 C1-3 vs 72D-5.txt

description:
GI_canc, Duodenal Tumor 72
Keywords = mouse gene expression database

source_name: GI_canc, Duo72


title: #24 C1-3 vs 48D-2-5.txt

description:
GI_canc, Duodenal Tumor 48
Keywords = mouse gene expression database

source_name: GI_canc, Duo48


title: T-ALL-1

source_name: Bone marrow sample


title: #40 C1-3 vs 59D-5.txt

description:
GI_canc, Duodenal Tumor 59
Keywords = mouse gene expression database

source_name: GI_canc, Duo59


title: C2C12 cells in proliferation #3

description:
C2C12 were cultered in low density to avoid confluence state. The cells were cultured in DMEM + 10% FCS medium for few passages.  RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, myoblaste, C2C12.

source_name: C2C12 preadipocyte cell line


title: T-LL-8


title: C2C12 cells in proliferation #2


title: 2ug/mL PA824: DMSO, 6h ( mAdb expid=45358 )

description:
H37Rv was grown to an OD650 of 0.3. At this stage, 50mL culture was treated with with 50uL drug at 2ug/mL (from 2mg/mL stock) or with equivalent amount of DMSO. RNA was extracted after 6h
array_print_batch : Mtbb-01
array_print_slide : mtbb1-38
mAdb_expid : 45358
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: C2C12 cells in proliferation #1


title: #42 C1-3 vs 43D-2-5.txt

description:
GI_canc, Duodenal Tumor 43
Keywords = mouse gene expression database

source_name: GI_canc, Duo43

source_name: Universal mouse reference RNA


title: #93 C1-3 vs 48D-5.txt


title: 0.4ug/mL PA824: DMSO, 6h ( mAdb expid=45356 )

description:
H37Rv was grown to an OD650 of 0.3. At this stage, 50mL culture was treated with with 50uL drug at 0.4ug/mL (from 0.4mg/mL stock) or with equivalent amount of DMSO. RNA was extracted after 6h
array_print_batch : Mtbb-01
array_print_slide : mtbb1-37
mAdb_expid : 45356
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: T-LL-7


title: 24ug/mL Clotrimazole: DMSO, 6h ( mAdb expid=44851 )

description:
H37Rv was grown in 7H9-based medium to an OD of 0.3 before treating 50mL culture with 24ug/mL clotrimazole (from 24mg/mL stock) or equivalent amount of DMSO for 6h
array_print_batch : Mtbb-01
array_print_slide : mtbb1-36
mAdb_expid : 44851
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Cltromazole


title: 20ug/mL chlorpromazine: DMSO, 6h ( mAdb expid=44857 )

description:
H37Rv was grown in 7H9-based medium to an OD of 0.3 before treating 50mL culture with 20ug/mL chlorpromazine (from 20mg/mL stock) or equivalent amount of DMSO for 6h
array_print_batch : Mtbb-01
array_print_slide : mtbb1-39
mAdb_expid : 44857
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Chlorpromazine


title: T-LL-6


title: #73 C1-3 vs 43D-5.txt


title: 24ug/mL clotrimazole: DMS, 6h ( mAdb expid=44850 )

description:
H37Rv was grown in 7H9-based medium to an OD of 0.3 before treating 50mL culture with 24ug/mL clotrimazole (from 24mg/mL stock) or equivalent amount of DMSO.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-35
mAdb_expid : 44850
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Clotrimazole


title: T-LL-5


title: T-LL-4


title: T-LL-3

description:
RNA extracted using Trizol.
Double round amplification completed with Arcturus RiboAmp kit.


title: 13ug/mL clofazimine: DMSO, 6h ( mAdb expid=44849 )

description:
H37Rv culture at an OD of 0.3 was treated for 6h with 13ug/mL clofazimine (from stock in DMSO) or with DMSO alone.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-34
mAdb_expid : 44849
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Clofazimine


title: Differentiated C2C12 day 7 #2

description:
C2C12 cells were cultered  to reach confluence. At confluence state, the cells were cultured in DMEM + 4% HS medium for seven days. Differentiation was estimate on the number and size polynucleated myotube cells. RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, myotubes,  C2C12.

source_name: C2C12 myoblaste cell line


title: Differentiated C2C12 day 7 #1


title: DuodTumor022YAFBV_dtb.txt

description:
GI_canc, Duodenal Tumor
Keywords = mouse gene expression database

source_name: GI_canc, Duo1


title: Isolated Peritoneal Macrophages #3

description:
Macrophages were isolated by washing the peritoneal cavity. Peritoneal cells were plated in DMEM-F12 + 10% NCS medium for 24h to remove non adherent cell types. RNA extraction was performed with TRIPURE reagents and protocol, lipids were removed just after adipocytes lysis into Tripure solution. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, Peritoneal macrophages

source_name: Peritoneal cavity


title: DuodTumor0225AFBW_dtb.txt


title: 13ug/mL clofazimine: DMSO, 6h ( mAdb expid=44848 )

description:
H37Rv was grown to an OD of 0.3 in normal 7H9-based medium. At this stage 50mL culture was treated with 50uL of either 13mg/mL clofazimine in DMSO or DMSO alone. RNA was extracted after 6h
array_print_batch : Mtbb-01
array_print_slide : mtbb1-33
mAdb_expid : 44848
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: T-LL-2


title: minimal medium (succinate): 7H9-based medium ( mAdb expid=44847 )

description:
H37Rv was grown to an OD of 0.3 in normal 7H9-based medium. At this stage culture was treated for 6h with 50uL DMSO/50mL culture followed by RNA extraction - this was labeled with Cy3. Another culture was grown in Minimal medium containing 10mM succinate as C-source and the RNA extracted at OD = 0.3 used for Cy5 labeling.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-32
mAdb_expid : 44847
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Min med (succinate)


title: Isolated Peritoneal Macrophages #2


title: Hgfu cells

description:
Hgfu were cultered in low density to avoid confluence state. The cells were cultured in DMEM + 10% FCS medium for few passages.  RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, white adipose tissue, preadipocyte, Hgfu.

source_name: Hgfu preadipocyte cell line


title: Isolated Peritoneal Macrophages #1


title: 20ug/mL Procept 6778: DMSO, 6h ( mAdb expid=44845 )

description:
H37Rv was grown in Sauton's medium to an OD of 0.3. At this stage 50mL culture was treated either with 50uL 20mg/mL Procept 6778/DMSO or with 50uL DMSO. RNA was extracted after 6h
array_print_batch : Mtbb-01
array_print_slide : mtbb1-30
mAdb_expid : 44845
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Procept 6778

source_name: DMSO


title: #23 C1-3 vs 72C-5.txt

description:
GI_canc, Col72
Keywords = mouse gene expression database

source_name: GI_canc, Col72


title: ColTum_022NAFD9_g8.txt

description:
Cancers; Colon Tumor
Keywords = mouse gene expression database

source_name: GI_canc, Col2


title: #25 C1-3 vs 43C-2-5.txt

description:
GI_canc, Col43
Keywords = mouse gene expression database

source_name: GI_canc, Col43


title: Ob1774 cells

description:
Ob1774 were cultered in low density to avoid confluence state. The cells were cultured in DMEM + 10% FCS medium for few passages.  RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, white adipose tissue, preadipocyte, Ob1774.

source_name: Ob1774 preadipocyte cell line


title: Minimal medium (Succinate): 7H9-based medium ( mAdb expid=44846 )

description:
H37Rv was grown to an OD of 0.3 in normal 7H9-based medium. At this stage culture was treated for 6h with 50uL DMSO/50mL culture followed by RNA extraction - this was labeled with Cy3. Another culture was grown in Minimal medium containing 10mM succinate as C-source and the RNA extracted at OD = 0.3 used for Cy5 labeling.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-31
mAdb_expid : 44846
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: #94 C1-3 vs 72C-2-5.txt


title: #56 C1-3 vs 43C-5.txt


title: T-LL-1

source_name: Lymphoma tissue


title: 3T3-F442A cells

description:
3T3-F442A were cultered in low density to avoid confluence state. The cells were cultured in DMEM + 10% FCS medium for few passages.  RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, white adipose tissue, preadipocyte, 3T3-F442A.

source_name: 3T3-F442A preadipocyte cell line


title: ColTum_022GAFD8_g8.txt

source_name: Universal mouse reference RNA


title: SW-620-2

city: Trento

first: Alessandro

last: Provenzani

address: via delle regole 101

department: CIBIO

country: Italy

institute: University of Trento

description:
SW620 colorectal cancer cell lines grown up to 60% of confluence, collected and lysed. Total RNA isolation following standard Affymetrix protocol
Keywords = colorectal cancer
Keywords = metastasis

source_name: SW620 cell extract


title: 10ug/mL #241: DMSO, 6h ( mAdb expid=44838 )

description:
H37Rv culture in 7H9-based medium was grown to an OD of 0.3. At this stage 50mL of culture was treated wither with 10ug/mL #241 (diamine analog made up to 10mg/mL in DMSO) or with equivalent amount of DMSO
array_print_batch : Mtbb-01
array_print_slide : mtbb1-2b
mAdb_expid : 44838
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 24ug/mL Econazole: DMSO, 6h ( mAdb expid=44839 )

description:
H37Rv culture in 7H9-based medium was grown to an OD of 0.3. At this stage 50mL of culture was treated either with 24ug/mL Econazole (24mg/mL stock in DMSO) or with equivalent amount of DMSO for 6h
array_print_batch : Mtbb-01
array_print_slide : mtbb1-28
mAdb_expid : 44839
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Econazole


title: SW-620-3


title: 3T3-L1 cells #2

description:
3T3-L1 were cultered in low density to avoid confluence state. The cells were cultured in DMEM + 10% FCS medium for few passages.  RNA extraction was performed with TRIPURE reagents and protocol. RNA were trated with DNASE before using them for the hybridization. cDNA were labeled with dCTP33P. Hybridization was performed according to the manufacturer protocol (Resgen). Quantification was performed with Imagene software.
Keywords = Mus musculus, white adipose tissue, preadipocyte, 3T3-L1.

source_name: 3T3-L1 preadipocyte cell line


title: ColonTum_022HAFC9_cta.txt

source_name: GI_canc, Col1


title: SW-620-1

description:
SW620 colorectal cancer cell lines grown up to 60% of confluence, collected and lysed. Total RNA isolation following standard Affymetrix protocol
Keywords = colorectal cancer
Keywords = metastasis
Lot batch =


title: SW-480-3

description:
SW480 colorectal cancer cell lines grown up to 60% of confluence, collected and lysed. Total RNA isolation following standard Affymetrix protocol
Keywords = colorectal cancer
Keywords = metastasis

source_name: SW480 cell extract


title: SW-480-1


title: SW-480-2


title: 3T3-L1 cells


title: 10ug/mL #59: DMSO, 6h ( mAdb expid=44724 )

description:
H37Rv at an OD of 0.3 was treated for 6h with 10ug/mL of the diamine analog #59 (from 10mg/mL stock in DMSO). Control culture was treated with 50uL DMSO per 50mL culture.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-3
mAdb_expid : 44724
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: ColonTum_022AAFC8_cta.txt


title: prors2_dark_6

city: Chicago

first: christos

last: Noutsos

country: Germany

institute: University of Chicago

description: Comparison of the dark adapted Arabidopsis prors2 mutant lacking prolyl tRNA synthetase versus the dark adapted WT. P. Pesaresi, D. Leister, unpublished

organism: Arabidopsis thaliana

source_name: WT, ecotype Columbia 0, dark adapted over night


title: prors2_dark_5


title: 10ug/mL #109: DMSO, 6h ( mAdb expid=44722 )

description:
H37Rv at an OD of 0.3 was treated for 6h with 10ug/mL of the diamine analog #109 (from 10mg/mL stock in DMSO). Control culture was treated with 50uL DMSO per 50mL culture.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-1
mAdb_expid : 44722
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: WT2_dark_4


title: prors2_dark_4


title: 50ug/mL Triclosan: EtOH ( mAdb expid=44721 )

description:
H37Rv at an OD of 0.3 was treated for 6h with 50ug/mL Triclosan (from 50mg/mL stock in EtOH). Control culture was treated with equivalent amount of EtOH.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-27
mAdb_expid : 44721
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: TRC

source_name: EtOH


title: 20ug/mL Procept 6776: DMSO, 6h ( mAdb expid=44718 )

description:
H37Rv was grown in Sauton's medium to an OD of 0.3. At this stage culture was treated with 50uL of 20mg/mL Procept 6776 compound in DMSO per 50mL culture. Control culture in Sauton's was treated with equivalent amount of DMSO
array_print_batch : Mtbb-01
array_print_slide : mtbb1-22
mAdb_expid : 44718
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Procept 6776


title: vip6_2

city: East Lansing

first: Sookyung

last: Oh

state: MI

department: Horticulture

institute: Michigan State University

description: Gene expression profiles of vip6 mutant plants.

source_name: 3 week-old vip6 mutant plants


title: WT2_dark_5


title: 50ug/mL Thioridazine: DMSO, 6h ( mAdb expid=44716 )

description:
H37Rv at OD 0.3 was treated for 6h with 50ug/mL thioridazine (from 50mg/mL stock in DMSO) whereas control culture was treated with equivalent amount of DMSO.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-12
mAdb_expid : 44716
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Thioridazine

source_name: DMSO


title: WT_2

description: Gene expression profiles of wild-type plants.

source_name: 3 week-old wild type Arabidopsis


title: WT2_dark_6


title: 20ug/mL Procept 6778: DMSO, 6h ( mAdb expid=44719 )

description:
H37Rv was grown in Sauton's medium to an OD of 0.3. At this stage culture was treated with 50uL of 20mg/mL Procept 6778 compound in DMSO per 50mL culture. Control culture (in Sauton's) was treated with equivalent amount of DMSO
array_print_batch : Mtbb-01
array_print_slide : mtbb1-25
mAdb_expid : 44719
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: WT_1


title: vip5_2

description: Gene expression profiles of vip5 mutant plants.

source_name: 3 week-old vip5 mutant plants


title: WT2_dark_3


title: 20ug/mL ethambutol: DMSO ( mAdb expid=44725 )

description:
H37Rv at an OD of 0.3 was treated for 6h with 20ug/mL of the diamine ethambutol (from fresh 20mg/mL stock in DMSO). Control culture was treated with 50uL DMSO per 50mL culture.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-4
mAdb_expid : 44725
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: EMB


title: prors2_dark_3


title: flk_ath1_exp3_f2

city: La Jolla

first: Todd

middle: C.

last: Mockler

state: CA

department: Plant Biology Laboratory

institute: The Salk Institute for Biological Studies

description: 7-day-old long-day grown flk. Tissues collected at 1hr after dawn.

source_name: flk


title: vip5_1


title: prors2_dark_2


title: flk_ath1_exp3_f1


title: 20ug/mL chlorpromazine: DMSO, 6h ( mAdb expid=44714 )

description:
H37Rv at OD 0.3 was treated for 6h with 20ug/mL chlorpromazine (from 20mg/mL stock in DMSO) whereas control culture was treated with equivalent amount of DMSO.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-23
mAdb_expid : 44714
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: CPZ


title: WT2_dark_2


title: 2.5mM Dinitrophenol: DMSO, 6h ( mAdb expid=44715 )

description:
H37Rv at OD 0.3 was treated for 6h with 2.5mM dinitrophenol (from 2.5M stock in DMSO). Control culture was treated with DMSO (50uL/50mL culture)
array_print_batch : Mtbb-01
array_print_slide : mtbb1-24
mAdb_expid : 44715
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: DNP


title: 1ug/mL #111895: DMSO, 12h ( mAdb expid=44711 )

description:
H37Rv at OD 0.3 was treated for 12h with 1ug/mL #111895 from 2mg/mL stock in DMSO whereas control culture was treated with equivalent amount of DMSO
array_print_batch : Mtbb-01
array_print_slide : mtbb1-7
mAdb_expid : 44711
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: 24ug/mL clotrimazole: DMSO, 6h ( mAdb expid=44713 )

description:
H37Rv at OD 0.3 was treated for 6h with 24ug/mL clotrimazole from 24mg/mL stock in DMSO. Control culture was treated with equivalent amount of DMSO. Each culture volume was 50mL.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-11
mAdb_expid : 44713
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Clotrimazole


title: 50ug/mL Triclosan: DMSO, 6h ( mAdb expid=44717 )

description:
H37Rv at OD of 0.3 was treated for 6h with 50ug/mL Triclosan (from 50mg/mL stock in EtOH) whereas control culture was treated with equivalent amount of solvent.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-21
mAdb_expid : 44717
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: prors2_dark_1


title: WT2_dark_1


title: prors1_dark_5

description: Comparison of the dark adapted Arabidopsis prors1 mutant lacking prolyl tRNA synthetase versus the dark adapted WT. P. Pesaresi, D. Leister, unpublished


title: WT1_dark_6


title: prors1_dark_6


title: 1ug/mL #111891: DMSO, 12h ( mAdb expid=44710 )

description:
H37Rv at OD 0.3 was treated for 12 h with 1ug/mL #111891 (from 2mg/mL stock in DMSO) whereas control culture was treated with DMSO.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-6
mAdb_expid : 44710
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: flk_ath1_exp2_f3

description: 16-day-old continuous-light-grown flk.


title: 100ug/mL Cephalexin: Ctrl, 6h ( mAdb expid=44720 )

description:
H37Rv was treated for 6h with 100ug/mL cephalexin (from filter sterilized stock in water). Control culture was treated with nothing.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-26
mAdb_expid : 44720
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Cephalexin

source_name: Ctrl


title: flk_ath1_exp3_c1

description: 7-day-old long-day grown Col-0. Tissues collected at 1hr after dawn.


title: flk_ath1_exp3_f3


title: vip6_1


title: flk_ath1_exp3_c3


title: 1ug/mL #121940: DMSO, 12h ( mAdb expid=44709 )

description:
H37Rv at OD 0.32 was treated for 12 h with 1ug/mL #121940 (from 2mg/mL stock in DMSO) whereas control culture was treated with equivalent amount of DMSO.
array_print_batch : Mtbb-01
array_print_slide : mtbb1-5
mAdb_expid : 44709
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642


title: WT1_dark_5


title: prors1_dark_4


title: flk_ath1_exp2_f2

description: 16-day-old continuous-light-grown flk.


title: flk_ath1_exp2_f1

description: 16-day-old continuous-light-grown flk.


title: C6SPGFPfast2

city: Muenster

first: Lars

last: Tatenhorst

address: Domagkstr. 19

institute: Institute of Neuropathology

description: Migration

organism: Rattus norvegicus

source_name: C6 rat glioma cell line


title: prors1_dark_3

source_name: WT, ecotype Columbia 0, dark adapted over night


title: flk_ath1_exp2_c2

description: 16-day-old continuous-light-grown Col-0.


title: WT1_dark_3


title: 10ug/mL clofazimine: DMSO, 6h ( mAdb expid=44712 )

description:
H37Rv at OD 0.3 was treated for 6h with 10ug/mL clofazimine (from 10mg/mL stock in DMSO) whereas control culture was treated with equivalent amount of DMSO
array_print_batch : Mtbb-01
array_print_slide : mtbb1-8
mAdb_expid : 44712
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Clofazimine


title: WT1_dark_4


title: prors1_dark_2


title: C6SPGFPfast1

description: Migration

source_name: C6 glioma cell line


title: C6SPGFPslow1

description: Migration


title: prors1_dark_1


title: WT1_dark_2


title: C6fast1

description: Migration


title: C6SPGFPslow2

description: Migration


title: C6fast2

description: Migration


title: WT1_dark_1


title: flk_ath1_exp1_c2

description: 16-day-old long-day grown Col-0. Tissues were collected at 16hrs after dawn.


title: flk_ath1_exp1_f3

description: 16-day-old long-day grown flk. Tissues were collected at 16hrs after dawn.


title: flk_ath1_exp1_c3


title: flk_ath1_exp1_c1


title: Retrovirus vector-infected alpha4-floxed MEFs

city: Philadelphia

first: Mei

last: Kong

state: PA

institute: University of Pennsylvania

description: alpha4-floxed MEFs were infected with MIGR1-GFP (Vec) and GFP-positive cells were sorted by flow cytometry 24 hours after infection. The total RNA  was extracted after 48 hours of Vec infection.

source_name: mouse embryonic fibroblast


title: flk_ath1_exp2_c1


title: flk_ath1_exp3_c2


title: C6slow2

description: Migration


title: Retrovirus Cre-infected alpha4-floxed MEFs

description: alpha4-floxed MEFs were infected with MIGR1-GFP-Cre (Cre) and GFP-positive cells were sorted by flow cytometry 24 hours after infection. The total RNA  was extracted after 48 hours of Cre infection.


title: flk_ath1_exp1_f2


title: C6slow1

description: Migration


title: BMDM

status: Public on Aug 31 2004

city: Mineola

first: Siham

middle: D

last: Accacha

address: 222, Station Plaza, suite 501

department: Medicine

institute: Winthrop University Hospital

description: bone marrow were isolated from 6-10 weeks old female  C57BL/6J mice. bone marrow cells were cultured with 10(-8) M calcitriol and 60 ng/ml of M-CSF for 10 days. Total RNA was extracted from bone marrow preparation using TRIZOL Reagent according to the manufacturer's instruction. All hybridization was caried out according to the GE array Q series kit (Super Array).

source_name: bone marrow grown with vitamin D and macrophage colony stimulating factor (M-CSF)


title: flk_ath1_exp2_c3


title: 24ug/mL Econazole: DMSO, 6h ( mAdb expid=44840 )

description:
H37Rv culture at an OD of 0.3 was treated with 24ug/mL econazole (from 24mg/mL stock in DMSO) or with equivalent amount of DMSO for 6h
array_print_batch : Mtbb-01
array_print_slide : mtbb1-29
mAdb_expid : 44840
Sample_label_ch1: Cy5
Sample_label_ch2: Cy3
Sample_value_type: log2 ratio
Sample_series_id: GSE1642

source_name: Econazole


title: SHRSP ARB 1

city: Hannover

first: Torsten

last: Kirsch

institute: Medical School Hannover

description: 6 week old SHRSP received 1% NaCl, Olmesartan (4 mg/kg body weight p.o. daily)  or Lisinopril (6 mg/kg body weight/day) in order to study influence of Angiotensin II on gene expression in cerebral microcapillaries

source_name: SHRSP brain capillaries


title: wt(zm)1

first: Jennifer

last: Nemhauser

department: PBIO

institute: Salk Institute

description: Seedlings were immersed in water for 2 hours

source_name: Five-day old light-grown Columbia wild type (Col-0) seedlings


title: flk_ath1_exp1_f1


title: yuccamock2

description: Seedlings were immersed in one-half-strength Murashige Minimal Organics Medium (Invitrogen, Carlsbad, CA)  for 2.5 hours

source_name: Ten-day old light-grown yucca seedlings


title: SHRSP control


title: BMD

description: bone marrow were isolated from 6-10 week old female C57BL/6J mice.Bone marrow cells were cultured with 10(-8) M calcitriol for 10 days. Total RNA was extracted from bone marrow preparation using TRIZOL Reagent according to the manufacturer's instruction. 5 micrograms of total RNA reverse transcribed and then labeled according to the super array GE array Q series kit.

source_name: Bone marrow grown with vitamin D.


title: SHRSP control 2


title: wt(zm)2


title: SHRSP ACEI 2


title: SHRSP ARB 2


title: yuccamock1


title: SHRSP ACEI


title: WTmock2

description: seedlings were immersed in one-half-strength Murashige Minimal Organics Medium (Invitrogen, Carlsbad, CA) for 2.5 hours

source_name: Ten-day old light-grown Columbia wild type (Col-0) seedlings


title: WholeFly 4

status: Public on Aug 24 2004

city: Glasgow

first: Julian

last: Dow

address: Anderso College Complex

department: Molecular and Integrative Physiology

country: United Kingdom

institute: University of Glasgow

description: 7 day adult Oregon R Drosophila melanogaster whole flies (mixed sexes)

organism: Drosophila melanogaster


title: supernatant 10 % 6h

status: Public on Aug 26 2004

city: Sophia Antipolis

first: Chimene

last: Moreilhon

institute: CNRS

description: epithelial cells were in contact with bacterial supernatant or control supernatant during 6h

source_name: control supernatant 10 % 6h

source_name: supernatant 10 % 6h


title: WTmock1

source_name: Ten-day old light-grown Columbia wild type (Col-0)


title: supernatant 10 % 9h

description: epithelial cells were in contact with bacterial supernatant or control supernatant during 9h

source_name: control supernatant 10 % 9h

source_name: supernatant 10 % 9h


title: WholeFly 5

source_name: 7 day adult Oregon R Drosophila melanogaster whole flies


title: supernatant 10 % 1h

description: epithelial cells were in contact with bacterial supernatant or control supernatant during 1h

source_name: control supernatant 10 % 1h

source_name: supernatant 10 % 1h


title: supernatant 10 % 24h

description: epithelial cells were in contact with bacterial supernatant or control supernatant during 24h

source_name: control supernatant 10 % 24h

source_name: supernatant 10 % 24h


title: WholeFly 6


title: supernatant 10% 3h

description: epithelial cells were in contact with bacterial supernatant or control supernatant during 3h

source_name: control supernatant 10 % 3h

source_name: supernatant 10 % 3h


title: WholeFly 2


title: Tubule 5

description: 7 day adult Oregon R Drosophila melanogaster Malpighian tubules (mixed sexes)


title: Tubule 6

source_name: 7 day adult Oregon R Drosophila melanogaster Malpighian tubules


title: Tubule 2

source_name: 7 day adult Drosophila melanogaster Malpighian tubules


title: Tubule 3


title: Tubule 4


title: WholeFly 3


title: gcn4+DTT vs. gcn4-untreated (3 of 3)

status: Public on Aug 19 2004

city: San Francisco

first: Chris

last: Patil

address: 600 16th Street, N312

department: Biochemistry and Biophysics

institute: UCSF

description: gcn4 mutant cells were either treated with DTT for 30 minutes or untreated. The value reported is the log2-fold change in gene expression after treatment.

organism: Saccharomyces cerevisiae

source_name: gcn4+DTT, 30 minutes

source_name: gcn4 (untreated)


title: gcn2+DTT vs. gcn2-untreated (1 of 3)

description: gcn2 mutant cells were either treated with DTT for 30 minutes or untreated. The value reported is the log2-fold change in gene expression after treatment.

source_name: gcn2+DTT, 30 minutes

source_name: gcn2 (untreated)


title: MonoMac6-LTD4-1h

status: Public on Aug 20 2004

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

institute: Ludwig Maximilians Universität München

description:
Mono-Mac-6 cells in RPMI-1640 containing 10% FCS stimulated with 100nM LTD4
Keywords = Leukotriene-Transcriptome
Keywords = Mono-Mac-6

source_name: Mono-Mac-6 cells


title: gcn4+DTT vs. gcn4-untreated (2 of 3)


title: gcn2+DTT vs. gcn2-untreated (2 of 3)


title: gcn4+DTT vs. gcn4-untreated (1 of 3)


title: ire1+DTT vs. ire1-untreated (2 of 3)

description: ire1 mutant cells were either treated with DTT for 30 minutes or untreated. The value reported is the log2-fold change in gene expression after treatment.

source_name: ire1+DTT, 30 minutes

source_name: ire1 (untreated)


title: ire1+DTT vs. ire1-untreated (3 of 3)


title: ire1+DTT vs. ire1-untreated (1 of 3)


title: Cy3 probe2 from aged oocyte RNA1 vs Cy5 probe2 from young oocyte RNA1

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

source_name: Cy3 probe2 from aged oocyte RNA1

source_name: Cy5 probe2 from young oocyte RNA1


title: MonoMac6-control-1h

description:
Mono-Mac-6 cells in RPMI-1640 containing 10% FCS stimulated with 0.05% ethanol
Keywords = Leukotriene-Transcriptome
Keywords = Mono-Mac-6


title: wt+DTT vs wt-untreated (2 of 3)

description: Wildtype cells were either treated with DTT for 30 minutes or untreated. The value reported is the log2-fold change in gene expression after treatment.

source_name: wildtype + DTT, 30 minutes

source_name: wildtype (untreated)


title: wt+DTT vs wt-untreated (3 of 3)


title: wt+DTT vs wt-untreated


title: HAC1proHI +DTT B

status: Public on Aug 18 2004

first: Jess

last: Leber

state: IL

address: 920 E. 58th Street CLSC 615

department: Microbiology

institute: The University of Chicago

description:
HAC1proHI +DTT, 60 min
B

source_name: reference mix

source_name: HAC1proHI +DTT


title: Cy3 probe2 from young oocyte RNA5 vs Cy5 probe2 from aged oocyte RNA2

source_name: Cy3 probe2 from young oocyte RNA5

source_name: Cy5 probe2 from aged oocyte RNA2


title: W303 +TM B

description:
W303 + TM, 60 min
B


title: Fibronectin 2

city: Pittsburgh

first: Jorge

middle: L

last: Sepulveda

address: S758 200 Lothrop

department: Pathology

institute: University of Pittsburgh

description:
Neonatal rat ventricular myocytes plated in fibronectin-coated dishes, incubated for 24 h with 10% serum and for next 48 h in serum-free medium
Keywords = Fibronectin hypertrophy

source_name: NRVM, Fibronectin-coated plates


title: Fibronectin 1


title: Control 2

description:
Neonatal rat ventricular myocytes plated in uncoated dishes, incubated for 24 h with 10% serum and for next 48 h in serum-free medium
Keywords = Fibronectin hypertrophy

source_name: NRVM, Uncoated plates


title: Cy3 probe2 from aged oocyte RNA3 vs Cy5 probe2 from young oocyte RNA2

source_name: Cy3 probe2 from aged oocyte RNA3

source_name: Cy5 probe2 from young oocyte RNA2


title: HAC1proWT +DTT B

description:
HAC1proWT +DTT, 60 min
B

source_name: HAC1proWT +DTT


title: HAC1proWT dT +DTT B

description:
HAC1proWT dT +DTT, 60 min
B

source_name: HAC1proWT dT +DTT


title: Cy3 probe1 from young oocyte RNA1 vs Cy5 probe1 from aged oocyte RNA1

source_name: Cy3 probe1 from young oocyte RNA1

source_name: Cy5 probe1 from aged oocyte RNA1


title: Cy3 probe2 from young oocyte RNA1 vs Cy5 probe2 from aged oocyte RNA1

source_name: Cy3 probe2 from young oocyte RNA1

source_name: Cy5 probe2 from aged oocyte RNA1


title: Cy3 probe2 from aged oocyte RNA2 vs Cy5 probe2 from young oocyte RNA5

source_name: Cy3 probe2 from aged oocyte RNA2

source_name: Cy5 probe2 from young oocyte RNA5


title: dhac1 +DTT B

description:
dhac1 + DTT, 60 min
B

source_name: dhac1 +DTT


title: Control 1