title: PLC/PRF/5, RAD18, 10nM, 48h

description:
PLC/PRF/5, RAD18, 10nM, 48h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.

source_name: PLC/PRF/5 cells

tag: cell line


title: Male NOD Lacrimal Gland_Male-2

status: Public on Feb 01 2009

type: RNA

city: Boston

first: David

middle: A

last: Sullivan

state: MA

address: 20 Staniford Street

country: USA

institute: Schepens Eye Research Institute

description: Lacrimal gland gene expression in male NOD mice.

hyb_protocol: Following fragmentation, 20 microg of cRNA were hybridized for 18 hr at 45C on a Affymetrix GeneChip Mouse Expression Array 430A using a Affymetrix hybridization oven. GeneChips were washed and stained with streptavidin-Alexa 647 and washed again using a Model 450 Fluidics station and Affymetrix GeneChip Operating Software (GCOS) .

scan_protocol: GeneChips were scanned with a Affymetrix Model 7000 scanner running GCOS v1.3 software.

data_processing: Data were analyzed with GCOS software using the default settings.  No normalization was performed.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Lacrimal glands from male NOD mice ( glands pooled from 5-8 mice)

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit

extract_protocol: RNA was purified with Trizol and RNAqueous spin columns following the manufacturer's instructions.

tag: Lacrimal glands from male NOD mice (glands pooled from 5-8 mice)


title: Female NOD Lacrimal Gland_Female-2

description: Lacrimal gland gene expression in female NOD mice.

source_name: Lacrimal glands from female NOD mice ( glands pooled from 5-8 mice)

tag: Lacrimal glands from female NOD mice (glands pooled from 5-8 mice)


title: Aromatase KO Lacrimal_Female 1

description: Lacrimal gland gene expression in female aromatase knockout mice.

source_name: Lacrimal glands from female aromatase knockout mice ( glands pooled from 5-8 mice)

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 2 microg total RNA using a CodeLink Expression Assay Reagent Kit.

tag: Lacrimal glands from female aromatase knockout mice (glands pooled from 5-8 mice)


title: Female NOD Lacrimal Gland_Female-1


title: HUH7, APOB-Hs3, 10nM, 12h

first: Julja

last: Burchard

address: 33 Avenue Louis Pasteur

department: Computational & Systems Biology

institute: Merck & Co., Inc.

description:
HUH7, APOB-Hs3, 10nM, 12h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.

hyb_protocol: GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques.  Arrays are hybridized for 18 hours at 45oC with vigorous mixing.   Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed.  Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.

scan_protocol: Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.

data_processing: Data were loaded into the Rosetta Resolver system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260).  Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value.  The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).

label: Biotin is incorporated during the amplification.  This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.

organism: Homo sapiens

source_name: HUH7 cells

label_protocol: The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin.  After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency.  The labeled molecules are biotinylated-cRNA.

extract_protocol: Samples are processed in parallel in 96-well plates to minimize potential variation.  Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.


title: Male MRL/lpr Lacrimal Gland_Male-2

description: Lacrimal gland gene expression in male MRL/lpr mice.

source_name: Lacrimal glands from male MRL/lpr mice ( glands pooled from 5-8 mice)

tag: Lacrimal glands from male MRL/lpr mice (glands pooled from 5-8 mice)


title: Male MRL/lpr Lacrimal Gland_Male-3


title: Male MRL/lpr Lacrimal Gland_Male-1


title: Male NOD Lacrimal Gland_Male-3


title: Female MRL/lpr Lacrimal Gland_Female-1

description: Lacrimal gland gene expression in female MRL/lpr mice.

source_name: Lacrimal glands from female MRL/lpr mice ( glands pooled from 5-8 mice)

tag: Lacrimal glands from female MRL/lpr mice (glands pooled from 5-8 mice)


title: Female NOD Lacrimal Gland_Female-3


title: Hepa1-6, APOB-Hs4, 10nM, 6h

description:
Hepa1-6, APOB-Hs4, 10nM, 6h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.

source_name: Hepa1-6 cells


title: Hepa1-6, APOB-Hs1, 10nM, 6h

description:
Hepa1-6, APOB-Hs1, 10nM, 6h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Hepa1-6, APOB-Hs3, 10nM, 12h

description:
Hepa1-6, APOB-Hs3, 10nM, 12h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Hepa1-6, APOB-Hs4, 10nM, 12h

description:
Hepa1-6, APOB-Hs4, 10nM, 12h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Female MRL/lpr Lacrimal Gland_Female-2


title: Female MRL/lpr Lacrimal Gland_Female-3


title: Hepa1-6, APOB-Hs1, 10nM, 24h

description:
Hepa1-6, APOB-Hs1, 10nM, 24h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Hepa1-6, APOB-Hs3, 10nM, 24h

description:
Hepa1-6, APOB-Hs3, 10nM, 24h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Hepa1-6, APOB-Hs1, 10nM, 12h

description:
Hepa1-6, APOB-Hs1, 10nM, 12h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Hepa1-6, APOB-Hs4, 10nM, 24h

description:
Hepa1-6, APOB-Hs4, 10nM, 24h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Wild-type_littermate_R3

status: Public on Jan 24 2009

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

description: cDNA prepared by Nugen Ovation Aminoallyl RNA amplification system

hyb_protocol: Hybridization of 2.5 mcg labeled cDNA to GeneChip Mouse Genome 430A 2.0 arrays was conducted following the recommendations of the array manufacturer (Affymetrix).

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring 7.2 program.

source_name: Total RNA from P0 (newborn) lens from the wild-type mice

label_protocol: The labeled mRNA/cDNA was prepared using Nugen Ovation Aminoallyl RNA amplification system

extract_protocol: LE-AP-2a and wildtype littermate P0 lenses were dissected and total RNA was isolated using the Qiagen Rneasy Mini Kit, according to manufacturer's instructions.

treatment_protocol: LE-AP-2a and wildtype littermate P0 lenses were dissected.

tag: Mouse carrying a wild-type copy of Tcfap2a and/or lacked the Le-Cre transgene


title: Mouse liver, APOB-Hs4-1, 3mpk, 3d

description:
Mouse liver, APOB-Hs4-1, 3mpk, 3d
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.

source_name: Mouse liver

tag: tissue

value: liver


title: Wild-type_littermate_R2


title: Mouse liver, APOB-Hs1-1, 3mpk, 3d

description:
Mouse liver, APOB-Hs1-1, 3mpk, 3d
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Wild Type (Aromatase KO) Meibomian_Male 2

description: Meibomian gland gene expression in male wild type (aromatase knockout) mice.

source_name: Meibomian glands from male wild type mice ( glands pooled from 5-8 mice)

tag: Meibomian glands from male wild type mice (glands pooled from 5-8 mice)


title: Mouse liver, APOB-Hs1-2, 3mpk, 3d

description:
Mouse liver, APOB-Hs1-2, 3mpk, 3d
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Mouse liver, APOB-Hs1-3, 3mpk, 3d

description:
Mouse liver, APOB-Hs1-3, 3mpk, 3d
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Hepa1-6, APOB-Hs1, 10nM, 48h

description:
Hepa1-6, APOB-Hs1, 10nM, 48h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Lens_RNA_from_Le-AP-2alpha_conditional_mutant_R2

source_name: Total RNA from P0 (newborn) lens from the Le-AP-2alpha (Tcfap2a gene) mutant mice

tag: Mouse carrying a recombined floxed Tcfap2a allele


title: Lens_RNA_from_Le-AP-2alpha_conditional_mutant_R3


title: Mouse liver, APOB-Hs4-2, 3mpk, 3d

description:
Mouse liver, APOB-Hs4-2, 3mpk, 3d
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Mouse liver, APOB-Hs3-3, 3mpk, 3d

description:
Mouse liver, APOB-Hs3-3, 3mpk, 3d
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Lens_RNA_from_Le-AP-2alpha_conditional_mutant_R1


title: Mouse liver, APOB-Hs4-3, 3mpk, 3d

description:
Mouse liver, APOB-Hs4-3, 3mpk, 3d
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Mouse liver, APOB-Hs3-2, 3mpk, 3d

description:
Mouse liver, APOB-Hs3-2, 3mpk, 3d
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Hepa1-6, APOB-Hs3, 10nM, 48h

description:
Hepa1-6, APOB-Hs3, 10nM, 48h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Hepa1-6, APOB-Hs4, 10nM, 48h

description:
Hepa1-6, APOB-Hs4, 10nM, 48h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: Mouse liver, APOB-Hs3-1, 3mpk, 3d

description:
Mouse liver, APOB-Hs3-1, 3mpk, 3d
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.


title: post-7d DMSO stimulation

status: Public on Jan 22 2009

first: Jessica

last: Mar

address: 44 Binney St Smith 822

department: Biostatistics & Computational Biology

institute: Dana-Farber Cancer Institute

description: Gene expression data from HL-60 cells exposed to DMSO for 7d.

hyb_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data were analyzed using the Microarray Suite (MAS) 5.0 software. Gene expression profiles for each sample were scaled by adjusting the average signal intensity of each array to a constant target intensity. Non-significantly expressed genes were filtered out based on the significance level of detection computed in MAS 5.0 from the variation of the signal within the 16 individual probes fo a probe set (p-value in MAS 5.0). Only genes detected as significantly expressed at type I error p < .03 were considered present, otherwise they were considered absent.

source_name: HL-60 progenitor cells after 7d of DMSO exposure

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

growth_protocol: HL-60 cells (ATCC) were cultured in IMDM medium (ATCC) supplemented with 15% fetal bovine serum in the absence of antibiotics.

extract_protocol: Total cellular RNA was isolated from frozen pellets using the RNAeasy kit (Qiagen), 8ug of each RNA sample was processed according to the Affymetrix protocol (Santa Clara, CA) for cRNA synthesis and labeling.

treatment_protocol: Cells of passage 7 (after receipt from ATCC) at a density of 1.5E-06/mL and growing at a rate of 1.2/day were treated with 1.25% DMSO or 1E-7M ATRA (both from Sigma) to induce differentiation. At each time point, 4E07 cells were harvested from the suspension culture, pelleted and immediately frozen in liquid nitrogen. Differentiation was monitored based on morphology in Giemsa stain, nitroblue tetrazolium-reducing activity and phagocytosis, and surface expression of CD11b in flow cytometry. A stationary state was reached at day 6 since the fraction of differentiated cells and the level of expression of CD11b did not further increase when cells were monitored up to day 12 after induction of differentiation.

tag: HL-60 progenitor cells


title: post-6d ATRA stimulation

description: Gene expression data from HL-60 cells exposed to ATRA for 6d.

source_name: HL-60 progenitor cells after 6d of ATRA exposure


title: post-7d ATRA stimulation

description: Gene expression data from HL-60 cells exposed to ATRA for 7d.

source_name: HL-60 progenitor cells after 7d of ATRA exposure


title: post-3d ATRA stimulation

description: Gene expression data from HL-60 cells exposed to ATRA for 3d.

source_name: HL-60 progenitor cells after 3d of ATRA exposure


title: post-8h DMSO stimulation

description: Gene expression data from HL-60 cells exposed to DMSO for 8h.

source_name: HL-60 progenitor cells after 8h of DMSO exposure


title: post-4d DMSO stimulation

description: Gene expression data from HL-60 cells exposed to DMSO for 4d.

source_name: HL-60 progenitor cells after 4d of DMSO exposure


title: post-5d ATRA stimulation

description: Gene expression data from HL-60 cells exposed to ATRA for 5d.

source_name: HL-60 progenitor cells after 5d of ATRA exposure


title: post-12h DMSO stimulation

description: Gene expression data from HL-60 cells exposed to DMSO for 12h.

source_name: HL-60 progenitor cells after 12h of DMSO exposure


title: post-3d DMSO stimulation

description: Gene expression data from HL-60 cells exposed to DMSO for 3d.

source_name: HL-60 progenitor cells after 3d of DMSO exposure


title: post-6d DMSO stimulation

description: Gene expression data from HL-60 cells exposed to DMSO for 6d.

source_name: HL-60 progenitor cells after 6d of DMSO exposure


title: post-4h DMSO stimulation

description: Gene expression data from HL-60 cells exposed to DMSO for 4h.

source_name: HL-60 progenitor cells after 4h of DMSO exposure


title: post-5d DMSO stimulation

description: Gene expression data from HL-60 cells exposed to DMSO for 5d.

source_name: HL-60 progenitor cells after 5d of DMSO exposure


title: post-2h DMSO stimulation

description: Gene expression data from HL-60 cells exposed to DMSO for 2h.

source_name: HL-60 progenitor cells after 2h of DMSO exposure


title: post-2d DMSO stimulation

description: Gene expression data from HL-60 cells exposed to DMSO for 2d.

source_name: HL-60 progenitor cells after 2d of DMSO exposure


title: post-18h DMSO stimulation

description: Gene expression data from HL-60 cells exposed to DMSO for 16h.

source_name: HL-60 progenitor cells after 18h of DMSO exposure


title: post-4d ATRA stimulation

description: Gene expression data from HL-60 cells exposed to ATRA for 4d.

source_name: HL-60 progenitor cells after 4d of ATRA exposure


title: post-1d DMSO stimulation

description: Gene expression data from HL-60 cells exposed to DMSO for 1d.

source_name: HL-60 progenitor cells after 1d of DMSO exposure


title: post-1d ATRA stimulation

description: Gene expression data from HL-60 cells exposed to ATRA for 1d.

source_name: HL-60 progenitor cells after 1d of ATRA exposure


title: Wild-type_littermate_R1

description: cDNA prepared by Nugen Ovation Aminoallyl RNA amplification system

source_name: Total RNA from P0 (newborn) lens from the wild-type mice


title: post-18h ATRA stimulation

description: Gene expression data from HL-60 cells exposed to ATRA for 16h.

source_name: HL-60 progenitor cells after 18h of ATRA exposure


title: post-8h ATRA stimulation

description: Gene expression data from HL-60 cells exposed to ATRA for 8h.

source_name: HL-60 progenitor cells after 8h of ATRA exposure


title: undifferentiated control

description: Gene expression data from undifferentiated HL-60 cells at 0h.

source_name: HL-60 progenitor cells at 0h, no exposure, undifferentiated control.


title: Hepa1-6, APOB-Hs3, 10nM, 6h

description:
Hepa1-6, APOB-Hs3, 10nM, 6h
siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.

source_name: Hepa1-6 cells


title: post-2h ATRA stimulation

description: Gene expression data from HL-60 cells exposed to ATRA for 2h.

source_name: HL-60 progenitor cells after 2h of ATRA exposure


title: post-4h ATRA stimulation

description: Gene expression data from HL-60 cells exposed to ATRA for 4h.

source_name: HL-60 progenitor cells after 4h of ATRA exposure


title: thymic lymphoma, HIF1a+/+, biological rep3

status: Public on Jan 12 2009

city: Philadelphia

first: M. Celeste

last: Simon

state: PA

address: 421 Curie Blvd.

institute: University of Pennsylvania

hyb_protocol: cDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC

scan_protocol: A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

data_processing: The data were analyzed with Partek Suite and normalized using GCRMA.

source_name: thymic lymphoma from HIF1a+/+, p53R270H/R270H mouse

label_protocol: 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated the T7 promoter sequence.  Second-strand cDNA synthesis was followed by in vitro transcription with T7 RNA polymerase for linear amplification of each transcript, and the resulting cRNA was converted to cDNA, fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

growth_protocol: HIF1a+/-, p53R270H/R270H, HIF1aKI/+; p53R270H/R270H; and HIF1a+/+, p53R270H/R270H mice were aged in a barrier facility until they developed signs of respiratory distress. Mice were then sacrificied and thymic lymphoma tissue collected and archived in RNAlater (Qiagen) at -80C.

extract_protocol: Trizol extraction as per manufacturer's instructions followed by purification on Qiagen RNeasy columns.

tag: Strain

value: mixed (C57BL/6-129/SvEvTac)

tag: Age:140 days


title: thymic lymphoma, HIF1a+/+, biological rep5

tag: Age:118 days


title: activated CD4+ T cell_plusIL-6-A

status: Public on Jan 17 2009

city: Burlington

first: Mercedes

last: Rincon

state: VT

address: 89 Beaumont Ave., Given D305

department: Medicine/Immunobiology program

institute: University of Vermont

hyb_protocol: biotin-labeled cRNA fragments that were hybridized to the genechip probe array at 45°C for 16 hr

scan_protocol: The probe arrays were scanned (Affymetrix GS3000 Scanner) to quantify the fluorescence intensity associated with each oligonucleotide probe.

data_processing:
Qspline normalization (Workman and coworkers),  RMA expression statistic
(Speed and coworkers).

label: Biotin

source_name: CD3/CD28-activated NK1.1-CD4+ T cells/IL-6 treated

label_protocol: Double-stranded cDNA was then synthesized from a T7-oligo(dT) primer followed by an in vitro transcription reaction (ENZO) and fragmentation reaction to produce biotin-labeled cRNA fragments that were hybridized to the probe array at 45°C for 16 hr.

growth_protocol: FACS-purified NK1.1-CD4+ T cells were activated with plate bound anti-CD3 (5ug/ml) and soluble anti-CD28 (1 ug/ml) in Bruff's medium in the presence of exogenous mIL-6 (100 ng/ml; R&D Systems) for 16 h.

extract_protocol: Total RNA was isolated with the RNAeasy Mini Kit (Qiagen) including an on-column DNaseI-digestion according to the manufacturer's protocol.

treatment_protocol: Cells from spleen and lymph nodes were depleted from CD8+, MHC II+, CD11b+ and NK1.1+ cells by negative selection; stained with anti-NK1.1-PE and anti-CD4-PE-Cy5.5 and purified by FACS-sorting into a NK1.1-CD4+ T cell  population (>99% purity).

tag: B10.BR strain

tag: female

tag: 7 weeks

tag: Cells from spleen and lymph nodes


title: liver from animals lacking apolipoprotein E with olive oil enriched diet

status: Public on Jan 20 2009

city: Zaragoza

first: Jesus

last: Osada

address: Miguel Servet, 177

country: Spain

institute: Universidad de Zaragoza

description: Gene expression data from liver apolipoprotein E-deficient female mice on a olive oil enriched diet for 4 weeks

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Murine Genome MOE430A 2.0

scan_protocol: GeneChips were scanned using the GeneArray Scanner (Agilent Technologies, Palo Alto, CA, USA

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Liver RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA

extract_protocol: Tri reagent extraction of total RNA was performed according to the manufacturer's instructions. RNA was extracted using a Quiagen RNeasy kit.

tag: Two-month old female Animals with a C57BL/6J genetic background were fed a refined olive oil (10%, w/w) and low cholesterol diet (0.04%, w/w).


title: animals lacking apolipoprotein E with maslinic acid containing olive oil enriched diet

description: Gene expression data from liver apolipoprotein E-deficient female mice on a maslinic acid-containing olive oil enriched diet for 4 weeks

tag: Two-month old female animals with a C57BL/6J genetic background were fed a refined olive oil enriched in 110 mg/kg maslinic acid (10%, w/w) and low cholesterol diet (0.04%, w/w).


title: thymic lymphoma, HIF1a+/+, biological rep4

tag: Age:106 days


title: activated CD4+ T cell_plusIL-6-C


title: thymic lymphoma, HIF1a+/+, biological rep2

tag: Age:121 days


title: activated CD4+ T cell_minusIL-6_ControlC

source_name: CD3/CD28-activated NK1.1-CD4+ T cells/IL-6 untreated

growth_protocol: FACS-purified NK1.1-CD4+ T cells were activated with plate bound anti-CD3 (5ug/ml) and soluble anti-CD28 (1 ug/ml) in Bruff's medium in the absence of exogenous mIL-6 (100 ng/ml; R&D Systems) for 16 h.


title: post-12h ATRA stimulation

description: Gene expression data from HL-60 cells exposed to ATRA for 12h.

source_name: HL-60 progenitor cells after 12h of ATRA exposure


title: activated CD4+ T cell_plusIL-6-B


title: thymic lymphoma, HIF1a+/+, biological rep1


title: thymic lymphoma, HIF1aKI/+, biological rep5

source_name: thymic lymphoma from HIF1aKI/+, p53R270H/R270H mouse

tag: Age:145 days


title: activated CD4+ T cell_minusIL-6_ControlB


title: thymic lymphoma, HIF1aKI/+, biological rep4

tag: Age:179 days


title: thymic lymphoma, HIF1aKI/+, biological rep3

tag: Age:71 days


title: thymic lymphoma, HIF1aKI/+, biological rep1

tag: Age:148 days


title: thymic lymphoma, HIF1a+/-, biological rep5

source_name: thymic lymphoma from HIF1a+/-, p53R270H/R270H mouse

tag: Age:125 days


title: thymic lymphoma, HIF1a+/-, biological rep4

tag: Age:132 days


title: thymic lymphoma, HIF1a+/-, biological rep3

tag: Strain

tag: Age:165 days


title: thymic lymphoma, HIF1a+/-, biological rep1


title: ET_cells_6h_Dioxane_1

status: Public on Dec 31 2008

city: Duesseldorf

first: Markus

last: Frericks

address: Auf'm Hennekamp 50

department: Immunology

country: Germany

institute: Institute for Environmental Research

description: ET-cells were treated with 0.05 %V 1.4_Dioxane for 4h

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Data was processed using RMA (affy-package, R 2.4)

label: PE

source_name: Fetal murine cortical thymic epithelial cell line

label_protocol: Affymetrix standard protocol

growth_protocol: The ET, fetal murine cortical thymic epithelial cell line, was cultivated to 80-90 % confluence on 24-well plates. Cells were cultivated in DMEM, glucose high, containing L-glutamine (PAA), was supplemented with 10% FCS and 1%pen/strep.

extract_protocol: Total RNA was isolated from 80-90% confluent ET cells using TRIzol and after insuring integrity processed after the Affymetrix standard protocol

treatment_protocol: 80-90% confluent ET cells were washed with PBS and treated 0.05 %V 1.4_Dioxane in DMEM (10%FCS, Glucose high). After 4h cells were washed with PBS and RNA isolated with TRIzol.

tag: Treatment

tag: Time

tag: Replicate


title: ET_cells_6h_TCDD_1

description: ET-cells were treated with 5 nM 2,3,7,8-Tetrachlodibenzo-p-dioxin (TCDD) for 6h

treatment_protocol: 80-90% confluent ET cells were washed with PBS and treated with 5 nM 2,3,7,8-Tetrachlodibenzo-p-dioxin (TCDD) in DMEM (10%FCS, Glucose high). After 6h cells were washed with PBS and RNA isolated with TRIzol.

tag: Fetal murine cortical thymic epithelial cell line


title: ET_cells_6h_Dioxane_2

treatment_protocol: 80-90% confluent ET cells were washed with PBS and treated with 0.05 %V 1.4_Dioxane in DMEM (10%FCS, Glucose high). After 4h cells were washed with PBS and RNA isolated with TRIzol.


title: TLR9 6hr

status: Public on Jan 01 2009

city: Cambridge

first: Mitchell

last: Guttman

address: 7 Cambridge Center

institute: Broad Institute

description: lincRNA Paired Samples

hyb_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

data_processing: RMA

source_name: BMDC Stimulated

growth_protocol: BMDC Protocol (see manuscript)

extract_protocol: Trizol

tag: BMDC TLR9 Stimulated


title: ET_cells_6h_TCDD_2

value: 5 nM 2,3,7,8-Tetrachlodibenzo-p-dioxin (TCDD)


title: BMDC Unstimulated 2hr

description: lincRNA Paired Samples

scan_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

source_name: BMDC Unstimulated

tag: Bone Marrow Dendridic Cells


title: thymic lymphoma, HIF1a+/-, biological rep2

tag: Age:203 days


title: BMDC Unstimulated 24hr

description: lincRNA Paired Samples

label_protocol: Standard Affymetrix protocols for Mouse Genome 430 2.0 Array


title: TLR4 6hr

description: lincRNA Paired Samples

tag: BMDC TLR4 Stimulated


title: BMDC Unstimulated 16hr

description: lincRNA Paired Samples


title: ET_cells_4h_TCDD_2

description: ET-cells were treated with 5 nM 2,3,7,8-Tetrachlodibenzo-p-dioxin (TCDD) for 4h

treatment_protocol: 80-90% confluent ET cells were washed with PBS and treated with 5 nM 2,3,7,8-Tetrachlodibenzo-p-dioxin (TCDD) in DMEM (10%FCS, Glucose high). After 4h cells were washed with PBS and RNA isolated with TRIzol.


title: TLR2 6hr

description: lincRNA Paired Samples

tag: BMDC TLR2 Stimulated


title: ET_cells_4h_TCDD_1


title: ET_cells_2h_Dioxane_1

description: ET-cells were treated with Dioxane for 2h

treatment_protocol: 80-90% confluent ET cells were washed with PBS and treated with 0.05% V 1.4-Dioxane in DMEM (10%FCS, Glucose high). After 2h cells were washed with PBS and RNA isolated with TRIzol.


title: ET_cells_4h_Dioxane_2

description: ET-cells were treated with Dioxane for 4h

treatment_protocol: 80-90% confluent ET cells were washed with PBS and treated with 0.05% V 1.4-Dioxane in DMEM (10%FCS, Glucose high). After 4h cells were washed with PBS and RNA isolated with TRIzol.


title: ET_cells_2h_TCDD_1

description: ET-cells were treated with TCDD for 2h

treatment_protocol: 80-90% confluent ET cells were washed with PBS and treated with 5nM TCDD in DMEM (10%FCS, Glucose high). After 2h cells were washed with PBS and RNA isolated with TRIzol.


title: ET_cells_2h_TCDD_2

description: ET-cells were treated with TCDD for 2h


title: ET_cells_4h_Dioxane_1


title: ET_cells_2h_Dioxane_2


title: xenograft  14 day human array replicate 2

status: Public on Dec 22 2008

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChipHuman U133A arrays.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip 2500 Scanner (Affymetrix).

data_processing: MAS5.0 was used for initial data extraction, raw data normalised to the internal spikes using R.  Human and mouse orthologues and homologues were identified using Netaffix and only those transcripts used for further analysis.

organism:
Homo sapiens
Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA and Qiagen RNeasy purification were performed according to the manufacturer's instructions.

tag: xenograft, day 14 post implantation on human chip


title: NCI-H460_AdFHIT_48hrs_exp2_rep2_sc1

status: Public on Dec 25 2008

city: Milan

first: Luca

last: Roz

address: Via Venezian 1

department: Experimental Oncology and Molecular Medicine

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description:
RNA was extracted from AdFHIT transduced H460 lung cancer cells harvested at 48 hours post infection at a multiplicity of infection of 10. Three independent infections were harvested and RNA preparations were pooled, transcribed into cDNA, labeled, and hybridized following the manufacturer's protocol to the oligonucleotide microarray Human Gene Chip HG-U95Av2 (Affymetrix). Two independent hybridizations were performed (rep1 and rep2) and scan images aquired before (sc1) and after (sc2) anti-streptavidin antibody enhancement step.
The whole procedure was repeated twice (starting from thawing of new aliquot of NCI-H460 cells) resulting in two independent experiments (exp1 and exp2).

hyb_protocol: 20 microg of fragmented biotin labeled cRNA target were used for Affymetrix GeneChip Array hybridization on HG-U95Av2 chip.

scan_protocol: The arrays were washed, stained and scanned according to Affymetrix protocols.

data_processing: All images were analyzed with MASv5.0

source_name: Lung cancer cell line NCI-H460, transduced with AdFHIT, 48 hrs

label_protocol: 10 microg of cDNA were then transcribed with In Vitro Transcription System (Ambion) using biotinylated CTP and UTP.

extract_protocol: TRIzol (Invitrogen Life Technologies) extraction, followed by cleanup in RNeasy columns (QIAGEN).

treatment_protocol: Transduced with adenoviral vector carrying human FHIT transgene (48 hrs)

tag: Cell line

value: NCI-H460 (ATCC HTB-177)

tag: Organ

value: lung

tag: Disease

value: carcinoma; large cell lung cancer

tag: Derived from metastatic site

value: pleural effusion


title: NCI-H460_AdLACZ_48hrs_exp2_rep2_sc1

description:
RNA was extracted from AdLACZ transduced H460 lung cancer cells harvested at 48 hours post infection at a multiplicity of infection of 10. Three independent infections were harvested and RNA preparations were pooled, transcribed into cDNA, labeled, and hybridized following the manufacturer's protocol to the oligonucleotide microarray Human Gene Chip HG-U95Av2 (Affymetrix). Two independent hybridizations were performed (rep1 and rep2) and scan images aquired before (sc1) and after (sc2) anti-streptavidin antibody enhancement step.
The whole procedure was repeated twice (starting from thawing of new aliquot of NCI-H460 cells) resulting in two independent experiments (exp1 and exp2).

source_name: Lung cancer cell line NCI-H460, transduced with AdLACZ, 48 hrs

treatment_protocol: Transduced with adenoviral vector carrying LacZ transgene (48 hrs)


title: NCI-H460_AdLACZ_48hrs_exp2_rep2_sc2


title: NCI-H460_AdFHIT_48hrs_exp2_rep1_sc2


title: NCI-H460_AdLACZ_48hrs_exp2_rep1_sc1

treatment_protocol: Transduced with adenoviral vector carrying LACZ transgene (48 hrs)


title: NCI-H460_AdLACZ_48hrs_exp2_rep1_sc2


title: NCI-H460_AdFHIT_48hrs_exp2_rep1_sc1


title: NCI-H460_AdFHIT_48hrs_exp2_rep2_sc2

description:
RNA was extracted from AdFhit transduced H460 lung cancer cells harvested at 48 hours post infection at a multiplicity of infection of 10. Three independent infections were harvested and RNA preparations were pooled, transcribed into cDNA, labeled, and hybridized following the manufacturer's protocol to the oligonucleotide microarray Human Gene Chip HG-U95Av2 (Affymetrix). Two independent hybridizations were performed (rep1 and rep2) and scan images aquired before (sc1) and after (sc2) anti-streptavidin antibody enhancement step.
The whole procedure was repeated twice (starting from thawing of new aliquot of NCI-H460 cells) resulting in two independent experiments (exp1 and exp2).


title: NCI-H460_AdFHIT_48hrs_exp1_rep1_sc2

description: RNA was extracted from AdFHIT transduced H460 lung cancer cells harvested at 48 hours post infection at a multiplicity of infection of 10. Three independent infections were harvested and RNA preparations were pooled, transcribed into cDNA, labeled, and hybridized following the manufacturer's protocol to the oligonucleotide microarray Human Gene Chip HG-U95Av2 (Affymetrix). Two independent hybridizations were performed (rep1 and rep2) and scan images aquired before (sc1) and after (sc2) anti-streptavidin antibody enhancement step.


title: NCI-H460_AdFHIT_48hrs_exp1_rep2_sc2


title: NCI-H460_AdLACZ_48hrs_exp1_rep2_sc2

description: RNA was extracted from AdLACZ transduced H460 lung cancer cells harvested at 48 hours post infection at a multiplicity of infection of 10. Three independent infections were harvested and RNA preparations were pooled, transcribed into cDNA, labeled, and hybridized following the manufacturer's protocol to the oligonucleotide microarray Human Gene Chip HG-U95Av2 (Affymetrix). Two independent hybridizations were performed (rep1 and rep2) and scan images aquired before (sc1) and after (sc2) anti-streptavidin antibody enhancement step.


title: activated CD4+ T cell_minusIL-6_ControlA

tag: B10.BR strain

tag: female

tag: 7 weeks

tag: Cells from spleen and lymph nodes


title: NCI-H460_AdLACZ_48hrs_exp1_rep2_sc1

description: RNA was extracted from AdLacZ transduced H460 lung cancer cells harvested at 48 hours post infection at a multiplicity of infection of 10. Three independent infections were harvested and RNA preparations were pooled, transcribed into cDNA, labeled, and hybridized following the manufacturer's protocol to the oligonucleotide microarray Human Gene Chip HG-U95Av2 (Affymetrix). Two independent hybridizations were performed (rep1 and rep2) and scan images aquired before (sc1) and after (sc2) anti-streptavidin antibody enhancement step.

data_processing: All images were analyzed with MASv5.0.


title: NCI-H460_AdFHIT_48hrs_exp1_rep1_sc1

description: RNA was extracted from AdFhit transduced H460 lung cancer cells harvested at 48 hours post infection at a multiplicity of infection of 10. Three independent infections were harvested and RNA preparations were pooled, transcribed into cDNA, labeled, and hybridized following the manufacturer’s protocol to the oligonucleotide microarray Human Gene Chip HG-U95Av2 (Affymetrix)

scan_protocol: The arrays were washed, stained and scanned according to Affymetrix protocols


title: S. pombe Rad21 binding pattern, G1 (cdc10-129)

type: genomic

city: Bethesda

first: Christine

middle: Katrin

last: Schmidt

state: MD

address: 41 Library Drive, Bldg. 41, C619

department: LRBGE

institute: NCI (NIH)

description: no additional information

hyb_protocol: Labeled DNA was hybridised to microarrays in an Affymterix Gene Chip Hybridisation Oven 640 for 16h at 42°C & 60rpm. For washing and staining the EukGe_WS1_v4_450 fluidics protocol was run on an Affymetrix Gene Chip Fluidics Station (version 450). Staining included one step with SAPE.

scan_protocol: Microarray scanning was performed with an Affymetrix Gene Chip Scanner 3000.

data_processing: The Affymetrix Gene Chip Operating Software GCOS, version 1.4,  was used for data processing.

label: biotin-11-ddATP (NEL548)

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Chromatin-immunoprecipitated DNA

label_protocol: DNA was labeled with biotin-11-ddATP using terminal transferase TdT (Roche, 400U/µl).

growth_protocol: Cells were arrested for 4 h at 36°C in EMM2 plus supplements in G1 using the thermosensitive cdc10-129 allele.

extract_protocol:
ChIP and microarray analysis were largely performed as described previously (Katou et al., 2003, see below). Essentially, 2 x 10^9 cells were fixed with 1% formaldehyde for 30 min at room temperature. Whole cell extracts were prepared using a multi-beads shocker (Yasui Kikai). Cell extracts were sonicated (Sanyo Soniprep 150) to fragment DNA into 400 - 800 bp long pieces which were processed for ChIP. Anti-Pk antibodies (SV5-Pk1, Serotec), in conjunction with protein-A coupled magnetic Dynabeads were used against the Pk-tagged cohesin subunit Rad21. Reversal of the cross-linking was achieved by incubating the eluted immunoprecipitates at 65°C overnight. Genomic DNA was purified and amplified by random PCR.
Reference:
Katou, Y., Kanoh, Y., Bando, M., Noguchi, H., Tanaka, H., Ashikari, T., Sugimoto, K. and Shirahige, K. (2003) S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex. Nature, 424, 1078-1083.

tag: strain


title: NCI-H460_AdLACZ_48hrs_exp1_rep1_sc2


title: post-2d ATRA stimulation

description: Gene expression data from HL-60 cells exposed to ATRA for 2d.

source_name: HL-60 progenitor cells after 2d of ATRA exposure

tag: HL-60 progenitor cells


title: NCI-H460_AdFHIT_48hrs_exp1_rep2_sc1

description: RNA was extracted from AdFhit transduced H460 lung cancer cells harvested at 48 hours post infection at a multiplicity of infection of 10. Three independent infections were harvested and RNA preparations were pooled, transcribed into cDNA, labeled, and hybridized following the manufacturer's protocol to the oligonucleotide microarray Human Gene Chip HG-U95Av2 (Affymetrix). Two independent hybridizations were performed (rep1 and rep2) and scan images aquired before (sc1) and after (sc2) anti-streptavidin antibody enhancement step.


title: NCI-H460_AdLacZ_48hrs_exp1_rep1_sc1


title: xenograft  7 day human array replicate 1

description: xenograft  7 day human array replicate 1

source_name: xenograft  7 day human array replicate 1

tag: xenograft, day 7 post implantation on human chip


title: xenograft  14 day human array replicate 1


title: xenograft  10 day human array replicate 1

tag: xenograft, day 10 post implantation on human chip


title: human endometrium time 0 human array replicate 1

description: human on human control

tag: time 0 control


title: xenograft  7 day human array replicate 2

description: xenograft  7 day human array replicate 2

source_name: xenograft  7 day human array replicate 2


title: xenograft  10 day human array replicate 2


title: human endometrium time 0 human array replicate 2

description: human on human control


title: mouse peritoneum time 0 human array replicate 1

description: mouse on human control

source_name: mouse peritoneumtime 0 human array replicate 1


title: Macrophage Mock Day4 Rep2

status: Public on Dec 15 2008

city: Gainesville

first: Maureen

middle: M.

last: Goodenow

state: FL

address: 1376 Mowry Road

department: Pathology, Immunology, & Laboratory Medicine

institute: University of Florida

hyb_protocol: Following fragmentation, Affymetrix human HG-U95Av2 oligonucleotide microarrays were hybridized for 16 hours at 45°C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4) in an Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip 3000 scanner.

data_processing: The arrays were analyzed with Microarray Suite version 4.0 (MAS 4.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Macrophages 4 days mock infected

label_protocol: cRNA synthesis was performed with 10 ug of total cellular RNA, according to Affymetrix Expression Analysis Technical Manual. Double-stranded cDNA were synthesized according to a standardized protocol (SuperScript double-stranded cDNA synthesis kit; Invitrogen, Carlbad, CA). cRNA were transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).

growth_protocol: Primary human monocyte-derived macrophages were maintained in RPMI 1640 (Gibco), 10% FBS (Gibco), 50 ug/ml Penn/Strep (Gibco) at 37°C, 5% CO2.

extract_protocol: Total RNA was extracted from macrophages using Qiagen's RNeasy Kit according to manufacturer's instructions.

treatment_protocol: HIV-1JRFL was grown up in human peripheral blood mononuclear cells (PBMCs). Supernatant from HIV+ and HIV- PBMCs were applied to macrophages for 24 hours. Macrophages were rinsed with 1X PBS, and fresh media was applied. 50% media changes occurred every other day until RNA was extracted from cells.


title: Macrophage Mock Day7 Rep2

source_name: Macrophages 7 days mock infected

tag: Primary human monocyte-derived macrophages


title: Macrophage Infected Day4 Rep3

source_name: Macrophages 4 days HIV-1 infected


title: Macrophage Mock Day4 Rep3


title: Macrophage Infected Day7 Rep3

source_name: Macrophages 7 days HIV-1 infected


title: Macrophage Mock Day2 Rep3

source_name: Macrophages 2 days mock infected


title: Macrophage Mock Day7 Rep1


title: Macrophage Infected Day2 Rep4

source_name: Macrophages 2 days HIV-1 infected


title: Macrophage Mock Day2 Rep4


title: Macrophage Mock Day4 Rep1


title: Macrophage Infected Day4 Rep1


title: Macrophage Infected Day7 Rep1


title: Macrophage Infected Day2 Rep3


title: Macrophage Infected Day4 Rep2


title: 05-0007_Septic Shock_day3_227

status: Public on Dec 12 2008

city: Cincinnati

first: Hector

middle: R

last: Wong

state: OH

address: 3333 Burnet Ave

department: Division of Critical Care Medicine

institute: CIncinnati Children's Hospital Medical Center

description: 1) Controls: 2) Septic shock; 3) Sepsis; 4) SIRS; 5) SIRS resolved

hyb_protocol: Create a hybridization cocktail for a single probe array that contains 0.05 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 0.1 mg/mL Herring Sperm DNA (Promega), 0.5 mg/mL Acetylated BSA (Invitrogen), and 1X Hybridization Buffer. Heat hybridization cocktail to 99°C for 5 minutes, to 45°C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45°C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45°C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics:  Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol EukGE-WS2v5_450. Arrays were stained with phycoerythrin-conjugated streptavidin [Molecular Probes, Eugene, OR] and hybridization signals were amplified using antibody amplification with goat IgG [Sigma-Aldrich] and anti-streptavidin biotinylated antibody [Vector Laboratories, Burlingame, CA], as described in the Affymetrix GeneChip® Expression Analysis Manual.

scan_protocol: Images were scanned using a Genechip scanner 3000 [Affymetrix]

data_processing:
Commercial Affymetrix Human Genome U133 Plus 2.0 GeneChip (Affymetrix, Santa Clara, CA). GeneChip CEL  files were subjected to RMA  normalization using  the  GeneSpring GX 7.1.
Standard Affymetrix internal control genes were used to check the quality of the assay by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and beta-actin, with acceptable 3' to 5' ratios between 1 and 3. Eukaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly.
GeneSpring 7.2 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering, filtering, and statistical analyses. The Raw CEL files were processed using the RMA (Robust Multichip Average) built in GeneSpring software. All the samples were then normalized to the median of the controls.

source_name: Septic Shock_day3

label_protocol: 120 ng of total RNA from 2 wild type [WT] and 4 beta-catenin knock-out [KO] pancreata at the 14.5 and 16.5 time points was amplified twice with the Arcturus RiboAmp kit [Arcturus Bioscience, Inc., Mountain View, CA] and cRNA was labeled with biotin-UTP, CTP using T7 RNA polymerase [Enzo Life Sciences, Inc., Farmingdale, NY].

extract_protocol:
Total RNA was extracted from whole blood using the PaxGene protocol.
Quality control steps: Total RNA was purified using RNeasy columns [Qiagen, Valencia, CA] according to the manufacturer’s directions and quality was assessed using an Agilent 2100 Bioanalyzer [Agilent Technologies, Inc., Palo Alto, CA].

treatment_protocol: Samples were not manipulated.

tag: Whole blood from normal children and children with SIRS, sepsis, or septic shock.


title: 04-0004_Septic Shock_day3_220


title: 15-0007_Septic Shock_day3_211


title: 15-0008_Septic Shock_day3_213


title: 11-0017_Septic Shock_day3_158


title: 10-0020_Septic Shock_day3_126


title: 06-0004_Septic Shock_day3_91


title: 05-0010_Septic Shock_day3_80


title: 05-0006_Septic Shock_day3_76


title: 09-0002_Septic Shock_day3_103


title: 10-0017_Septic Shock_day3_125


title: 01-0025_Septic Shock_day3_32


title: 04-0003_Septic Shock_day3_69


title: 05-0007_Septic Shock_day1_226


title: 01-0019_Septic Shock_day3_26


title: 25-070603_Septic Shock_day1_223


title: 01-0030_Septic Shock_day3_38


title: 15-0008_Septic Shock_day1_212


title: 15-0007_Septic Shock_day1_210


title: 04-0004_Septic Shock_day1_219


title: 17-0001A_Septic Shock_day1_216


title: 15-0012A_Septic Shock_day1_202


title: 15-0004_Septic Shock_day1_207


title: 15-0004_Septic Shock_day3_208


title: 12-0002A_Septic Shock_day1_188


title: 11-0054A_Septic Shock_day1_182


title: 13-0002A_Septic Shock_day1_191


title: 11-0017_Septic Shock_day1_157


title: 15-0011A_Septic Shock_day1_201


title: 11-0057A_Septic Shock_day1_184


title: 11-0029_Septic Shock_day1_168


title: 14-0004A_Septic Shock_day1_197


title: 14-0002A_Septic Shock_day1_195


title: 10-0020_Septic Shock_day1_127


title: 10-0012_Septic Shock_day1_120


title: 10-0021A_Septic Shock_day1_104


title: 11-0001_Septic Shock_day1_142


title: 09-0001_Septic Shock_day1_100


title: 10-0017_Septic Shock_day1_124


title: 09-0002_Septic Shock_day1_102


title: 06-0003_Septic Shock_day3_89


title: 07-0002_Septic Shock_day1_95


title: Macrophage Mock Day7 Rep3


title: Macrophage Infected Day7 Rep2


title: 06-0004_Septic Shock_day1_90


title: 11-0029_Septic Shock_day3_169


title: 05-0006_Septic Shock_day1_75


title: 06-0009A_Septic Shock_day1_83


title: 06-0003_Septic Shock_day1_88


title: 02-0002A_Septic Shock_day1_61


title: 06-0001_Septic Shock_day1_85


title: 06-0006_Septic Shock_day1_92


title: 05-0008_Septic Shock_day1_77


title: 04-0003_Septic Shock_day1_68


title: 07-0006A_Septic Shock_day1_99


title: 05-0010_Septic Shock_day1_79


title: 02-0001_Septic Shock_day1_59


title: 01-0052A_Septic Shock_day1_54


title: 01-0049A_Septic Shock_day1_48


title: 01-0053A_Septic Shock_day1_55


title: 06-0006_Septic Shock_day3_93


title: 01-0045A_Septic Shock_day1_43


title: 01-0051A_Septic Shock_day1_52


title: 01-0025_Septic Shock_day1_31


title: 01-0033A_Septic Shock_day1_39


title: 01-0030_Septic Shock_day1_37


title: 01-0024_Septic Shock_day1_29


title: 01-0019_Septic Shock_day1_27


title: 01-0058A_Septic Shock_day1_10


title: 01-0061A_Septic Shock_day1_15


title: 01-0066A_Septic Shock_day1_21


title: 01-0044A_Septic Shock_day1_9


title: 01-0007A_Septic Shock_day1_0


title: 09-0001_Sepsis_day3_101


title: 01-0059A_Septic Shock_day1_12


title: 01-0060A_Septic Shock_day1_14


title: 10-0004_Sepsis_day3_112


title: 10-0012_Sepsis_day3_121


title: 01-0043A_Sepsis_day1_7


title: 06-0001_SIRS resolved_day3_86

source_name: SIRS resolved_day3


title: 10-0004_Sepsis_day1_111


title: 02-0001_SIRS resolved_day3_60


title: 07-0002_SIRS resolved_day3_96


title: 05-0008_SIRS resolved_day3_78


title: 11-0001_SIRS resolved_day3_143


title: 01-0036A_Septic Shock_day1_3


title: 01-0024_SIRS resolved_day3_30


title: 15-0003_Control_day1_206


title: 15-0005_Control_day1_209


title: 25-070603_SIRS_day3_221


title: 15-0002_Control_day1_205


title: 15-0001_Control_day1_204


title: 01-0026_SIRS resolved_day3_34


title: 11-0037_Control_day1_173


title: 10-0029A_SIRS_day1_108


title: 11-0019_Control_day1_160


title: 11-0027_Control_day1_167


title: 01-0026_Septic Shock_day1_33


title: 11-0020_Control_day1_161


title: 11-0008_Control_day1_146


title: 11-0018_Control_day1_159


title: 11-0013_Control_day1_151


title: 11-0009_Control_day1_147


title: 11-0012_Control_day1_150


title: 500nm silica at high dose, rep3

status: Public on Dec 11 2008

city: Richland

first: Katrina

middle: M

last: Waters

state: WA

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

description: Mouse macrophage cells were treated with two sizes of amorphous silica particles at three doses for 2 hours.

hyb_protocol: Biotin-labeled cRNA (15ug) was fragmented to a size range between 50-200 bases and used for array hybridization with Affymetrix reagents.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Data were processed with RMA background correction and quantile normalization using Bioconductor packages

source_name: Cells exposed to 500nm silica at 1000ug/ml

label_protocol: cDNA was synthesized from 5ug of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA using Affymetrix reagents.

growth_protocol: Cells were plated in 24-well plates at a density of 75,000 cells/well and allowed to attach and grow for 24 hours in complete medium (DMEM supplemented to 10% fetal bovine serum and penicillin/streptomycin)

extract_protocol: Cells were lysed and RNA was prepared using the RNeasy kit from Qiagen (Valencia, CA)

treatment_protocol: Cells were plated in 60mm plates (7.5X105 cells) overnight in complete medium and then exposed to particles for 2hrs in serum-free medium.

tag: RAW 264.7 macrophage cells


title: 11-0011_Control_day1_149


title: 500nm silica at high dose, rep1


title: 500nm silica at mid dose, rep1

source_name: Cells exposed to 500nm silica at 500ug/ml


title: 500nm silica at mid dose, rep2


title: 500nm silica at mid dose, rep3


title: 500nm silica at low dose, rep2

source_name: Cells exposed to 500nm silica at 250ug/ml


title: 500nm silica at high dose, rep2


title: 11-0014_Control_day1_152


title: 500nm silica at low dose, rep3


title: 10nm silica at high dose, rep3

source_name: Cells exposed to 10nm silica at 50ug/ml


title: 10nm silica at mid dose, rep3

source_name: Cells exposed to 10nm silica at 20ug/ml


title: 10nm silica at low dose, rep3

source_name: Cells exposed to 10nm silica at 5ug/ml


title: 10nm silica at high dose, rep2


title: 10nm silica at high dose, rep1


title: 10nm silica at low dose, rep1


title: 10nm silica at low dose, rep2


title: 220_SPOR

status: Public on Dec 10 2008

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: Gene expression data from paraganglioma

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix hu95a v2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data files of all arrays were normalized using sequence information in Robust Multi_Chip Average (RMA) method.

source_name: head and neck paraganglioma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: Mutation

value: SPOR


title: Untreated cells, rep1

source_name: Untreated cells


title: Untreated cells, rep2


title: 199_SPOR

description: Gene expression data from paraganglioma


title: 170_SPOR

description: Gene expression data from paraganglioma


title: 500nm silica at low dose, rep1


title: 217_SPOR

description: Gene expression data from paraganglioma


title: 10nm silica at mid dose, rep2


title: 177_SPOR

description: Gene expression data from paraganglioma


title: Untreated cells, rep3


title: 137_SPOR

description: Gene expression data from paraganglioma


title: 189_SPOR

description: Gene expression data from paraganglioma


title: 201_SDHD

description: Gene expression data from paraganglioma

value: SDHD


title: N7543_PGL2

description: Gene expression data from paraganglioma


title: 200_SDHD

description: Gene expression data from paraganglioma


title: 185_SDHD

description: Gene expression data from paraganglioma


title: N7544_PGL2

description: Gene expression data from paraganglioma


title: 174_SDHD

description: Gene expression data from paraganglioma


title: 184_SDHD

description: Gene expression data from paraganglioma


title: N9357_PGL2

description: Gene expression data from paraganglioma


title: Intestine DBZ 5 days rep1

status: Public on Dec 04 2008

city: New York

first: Adolfo

last: Ferrando

state: NY

address: 1130 St Nicholas Ave Irving Cancer Research Center 5-505A

department: Institute for Cancer Genetics

institute: Columbia University

description: Inhibition of Notch signaling with DBZ induces secretory metaplasia of the gut

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: small intestine

label_protocol: Approximately 15 micrograms of total RNA were processed to produce biotinylated cRNA targets.

growth_protocol: Mice were treated with the gamma secretase inhibitor  DBZ (10 microM/kg) for 5 days via IP injection daily.

extract_protocol: RNA was extracted with Trizol following the manufacturer specifications

treatment_protocol: Small intestine was snap frozen immediately after collection and stored in liquid nitrogen prior to RNA extraction

tag: Tissue

value: small intestine


title: Intestine control (DMSO) 5 days rep2

description: unprocessed small intestine

growth_protocol: Mice were treated with DMSO (vehicle only control) for 5 days via IP injection daily

extract_protocol:
RNA was extracted with Trizol following the manufacturer specifications
biotin


title: Intestine dexa 5 days rep2

description: unprocessed small intestine

growth_protocol: Mice were treated with dexamethasone (15 mg/kg) for 5 days via IP injection daily


title: 173_SDHD

description: Gene expression data from paraganglioma


title: 144_PGL2

description: Gene expression data from paraganglioma


title: Tlx(f/Z)+4OH-TM60h-1

status: Public on Dec 01 2008

city: Dallas

first: Chun-Li

last: Zhang

state: TX

address: 6000 Harry Hines Blvd

institute: UT Southwestern

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: MAS5.0 and set Target Intensity of all probe sets to 200

source_name: mouse adult neural stem cells Tlx(f/Z)+4OH-TM 60hr

label_protocol: ENZO BioArray™ HighYield™ RNA Transcript Labeling Kit

extract_protocol: Invitrogen TRIzol


title: Intestine dexa+DBZ 5 days rep2

description: Inhibition of Notch signaling with DBZ induces secretory metaplasia of the gut, cotreatment with dexamethasone protects from DBZ induced gut toxicity

growth_protocol: Mice were treated with dexamethasone (15 mg/kg) and the gamma secretase inhibitor  DBZ (10 microM/kg) for 5 days via IP injection daily.


title: Intestine DBZ 5 days rep2


title: Intestine control (DMSO) 5 days rep1

description: unprocessed small intestine

growth_protocol: Mice were treated with DMSO (vehicle only treatment control) for 5 days via IP injection daily


title: Intestine dexa+DBZ 5 days rep1


title: Tlx(f/Z)+4OH-TM60h-2

tag: mouse adult neural stem cells Tlx(f/Z)+4OH-TM 60hr


title: Intestine dexa 5 days rep1

description: unprocessed small intestine

label_protocol: standard Affymetrix procedures

extract_protocol: Approximately 15 micrograms of total RNA were processed to produce biotinylated cRNA targets.

treatment_protocol: Small intestine was snap frozen  immediatly after collection and stored in liquid nitrogen prior to RNA extraction


title: Tlx(f/Z;CreER)+4OH-TM60h-1

source_name: mouse adult neural stem cells Tlx(f/Z;CreER)+4OH-TM 60hr


title: Tlx(f/Z)+4OH-TM36h-1

source_name: mouse adult neural stem cells Tlx(f/Z)+4OH-TM 36hr


title: Tlx(f/Z)+vehicle60h-2

source_name: mouse adult neural stem cells Tlx(f/Z)+vehicle 60hr


title: Tlx(f/Z;CreER)+vehicle36h-2

source_name: mouse adult neural stem cells Tlx(f/Z;CreER)+vehicle 36hr


title: Tlx(f/Z;CreER)+4OH-TM60h-2

tag: mouse adult neural stem cells Tlx(f/Z;CreER)+4OH-TM 60hr


title: Tlx(f/Z)+vehicle60h-1

tag: mouse adult neural stem cells Tlx(f/Z)+vehicle 60hr


title: 10nm silica at mid dose, rep1


title: Tlx(f/Z)+vehicle36h-2

source_name: mouse adult neural stem cells Tlx(f/Z)+vehicle 36hr


title: Tlx(f/Z;CreER)+4OH-TM36h-1

source_name: mouse adult neural stem cells Tlx(f/Z;CreER)+4OH-TM 36hr


title: Tongue 043 Normal

status: Public on Nov 14 2008

first: Nicholas

middle: D

last: Socci

address: 1275 York Ave

department: Computational & Systems Biology Program

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Fifteen ug of labeled cRNA was fragmented and then hybridized against the Affymetrix HG_U95Av2 oligonucleotide arrays (Affymetrix, Santa Clara, CA).

scan_protocol: Gene chips were scanned using the standard Affymetrix supplied scaner

data_processing: Date was processed using the standard Mas5.0 algorithm using the implementation in the Biocondutor Affy package

source_name: Normal

label_protocol: Five to 10 ug of total RNA were reverse transcribed in presence of an oligo dT-T7 primer.  The cDNA was used for the in vitro transcription amplification reaction in presence of biotinylated nucleotides.

extract_protocol: Total RNA from snap-frozen tissue samples from the 37 patients, was extracted with TRIsolTM reagent (Gibco BRL) following the manufacturer’s protocol and re-purified by the RNAeasy Mini-spin column (Qiagen).

value: Tongue


title: Tlx(f/Z;CreER)+vehicle60h-1

source_name: mouse adult neural stem cells Tlx(f/Z;CreER)+vehicle 60hr


title: Tlx(f/Z)+4OH-TM36h-2

tag: mouse adult neural stem cells Tlx(f/Z)+4OH-TM 36hr


title: Tlx(f/Z)+vehicle36h-1

tag: mouse adult neural stem cells Tlx(f/Z)+vehicle 36hr


title: Tlx(f/Z;CreER)+4OH-TM36h-2

tag: mouse adult neural stem cells Tlx(f/Z;CreER)+4OH-TM 36hr


title: T140C-GFP-positive

status: Public on Nov 28 2008

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

institute: IRCCS Ospedale Policlinico San Martino

hyb_protocol: Fragmented cRNA from two samples was hybridized to the mouse 430a2 array for 16 hours at 45 Celsius.The array was then washed and stained with streptavidin-phycoerythrin (SAPE) using the fluidics station

scan_protocol: Scanned with GeneChip Scanner 3000

data_processing: Expression values were extracted with RMA and merged in a dataset including all three independent tumor samples (T118D,T140C,T41F) as well as the public available data from GSE9566 series from Cahoy et al. Quantile normaliztion of the dataset was then performed at probeset level by using the affyPLM 1.16.0 package.

source_name: GFP-expressing cells from glioma induced by PDGF-B viral transduction

label_protocol:
One-Cycle Target Labelling Assay:
Biotinylated cRNA was prepared and fragmented according to the Affymetrix protocol.

extract_protocol: Cultures from tumors were established microdissecting GFP-positive areas under the fluorescence microscope, and trypsinizing them for 20 minutes. All tumor cultures were maintained in DME-F12 additioned with B27 supplement and human recombinant FGF2 and EGF (20 ng/ml, Invitrogen) and plated on to Matrigel coated flasks (1:200; BD Biosciences).

treatment_protocol: FACSorted in PBS/EDTA, centrifuged and resuspended in Trizol

tag: Cultured cells derived from gliomas induced by the retroviral transduction of a PDGF-b-IRES-eGFP construct. Source C57-BL6 mouse. The original glioma histopathologically resembled glioblastoma but immunostaining showed it was GFAP-negative, NG2-positive, Olig2-positive, PDGF-R-alpha- positive, CC1-immunoreactive, characterizing it as a high grade oligodendroglioma.


title: Tongue 042 Tumor

source_name: Tumor


title: T118D-GFP-positive

growth_protocol: Cultures from tumors were established microdissecting GFP-positive areas under the fluorescence microscope, and trypsinizing them for 20 minutes. All tumor cultures were maintained in DME-F12 additioned with B27 supplement and human recombinant FGF2 and EGF (20 ng/ml, Invitrogen) and plated on to Matrigel coated flasks (1:200; BD Biosciences).

extract_protocol:
Total RNA was extracted following the double extraction protocol: RNA isolation by acid
guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen) followed by a Qiagen
RNeasy clean-up procedure.


title: Tlx(f/Z;CreER)+vehicle36h-1

tag: mouse adult neural stem cells Tlx(f/Z;CreER)+vehicle 36hr


title: Tlx(f/Z;CreER)+vehicle60h-2

tag: mouse adult neural stem cells Tlx(f/Z;CreER)+vehicle 60hr


title: Tongue 042 Normal


title: T41F-GFP-positive


title: Tongue 041 Tumor


title: Tongue 038 Normal


title: Tongue 035 Normal


title: Tongue 040 Tumor


title: Tongue 030 Normal


title: Tongue 038 Tumor


title: Tongue 030 Tumor


title: Tongue 029 Tumor


title: Tongue 036 Tumor


title: Tongue 033 Tumor


title: Tongue 039 Normal


title: Tongue 027 Tumor


title: Tongue 029 Normal


title: Tongue 028 Tumor


title: Tongue 031 Tumor


title: Tongue 039 Tumor


title: Tongue 028 Normal


title: Tongue 034 Normal


title: Tongue 025 Tumor


title: Tongue 041 Normal


title: Tongue 025 Normal


title: Tongue 024 Normal


title: Tongue 021 Tumor


title: Tongue 018 Tumor


title: Tongue 017 Tumor


title: Tongue 016 Normal


title: Tongue 015 Normal


title: Tongue 013 Normal


title: Tongue 020 Normal


title: Tongue 017 Normal


title: Tongue 016 Tumor


title: Tongue 020 Tumor


title: Tongue 010 Tumor


title: Tongue 010 Normal


title: Tongue 013 Tumor


title: Tongue 015 Tumor


title: Tongue 009 Tumor


title: Tongue 011 Tumor


title: Tongue 012 Normal


title: Tongue 019 Normal


title: Tongue 009 Normal


title: Tongue 023 Tumor


title: Tongue 005 Normal


title: Tongue 006 Tumor


title: Tongue 007 Normal


title: Tongue 003 Tumor


title: Tongue 003 Normal


title: Tongue 002 Normal


title: Tongue 004 Normal


title: Tongue 001 Tumor


title: Tongue 007 Tumor


title: Tongue 002 Tumor


title: Tongue 004 Tumor


title: Tongue 005 Tumor


title: RNA expression profiles in cycling C2C12 cells

status: Public on Nov 06 2008

first: Brian

last: Dynlacht

department: Cancer Institute

institute: NYU Medical Center

description: gene expression profiles in murine cycling C2C12 cells

hyb_protocol: see manufacturer's web site

scan_protocol: see manufacturer's web site

data_processing: Raw data were normalized and quantified using dCHIP

source_name: The C2C12 murine myoblast cell line (obtained from ATCC)

label_protocol: see manufacturer's web site

growth_protocol: C2C12 cells were grown in DMEM supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was isolated from cells using Trizol (Invitrogen), and mRNA was amplified from 8 µg of total RNA. Labeling of cRNA and hybridization to Affymetrix mouse 430A_v2 GeneChips were performed according to the manufacturer's instructions. Each experiment was performed in triplicate.


title: MEF-1113-3-Ts19-rep_1

status: Public on Nov 05 2008

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

hyb_protocol: Following fragmentation, 18 ug of cRNA were hybridized for 16 hr at 45C on Mouse 430A_2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G scanner.

data_processing: Bioconductor Affy package and gcRMA

source_name: Mouse Embryo Fibroblast (MEF) with 3 copies of chromosome 19

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA according to the Affymetrix Expression Analysis Technical Manual.

growth_protocol: MEFs grown in DMEM, 10%FCS, 5mM Glutamine, Pen/Strep in humidified chamber at 37Deg C for 2 Passages

extract_protocol: Trizol according to the manufacturer's protocol

tag: MEFs grown in DMEM, 10%FCS, 5mM Glutamine, Pen/Strep in humidified chamber at 37Deg C  For 2 Passages with 3 copies of chromosome 19


title: MEF-836-1-Wt-rep_9

source_name: Mouse Embryo Fibroblast (MEF) with a normal complement of chromosomes

tag: MEFs grown in DMEM, 10%FCS, 5mM Glutamine, Pen/Strep in humidified chamber at 37Deg C  For 2 Passages with a normal complement of chromosomes


title: MEF-836-3-Ts1-rep_1

source_name: Mouse Embryo Fibroblast (MEF) with 3 copies of chromosome 1

tag: MEFs grown in DMEM, 10%FCS, 5mM Glutamine, Pen/Strep in humidified chamber at 37Deg C  For 2 Passages with 3 copies of chromosome 1


title: RNA expression profiles in differentiated C2C12 cells

description: gene expression profiles in murine differentiated C2C12 cells

growth_protocol: C2C12 cells were grown in DMEM supplemented with 10% fetal bovine serum. Differentiated cells were obtained by culturing confluent C2C12 cells in DMEM supplemented with 2% horse serum. Differentiated cells were separated from undifferentiated cells using diluted trypsin.

tag: The C2C12 murine myoblast cell line (obtained from ATCC)


title: MEF-1113-2-Wt-rep_8


title: MEF-666-5-Ts13-rep_4

source_name: Mouse Embryo Fibroblast (MEF) with 3 copies of chromosome 13

tag: MEFs grown in DMEM, 10%FCS, 5mM Glutamine, Pen/Strep in humidified chamber at 37Deg C  For 2 Passages with 3 copies of chromosome 13


title: MEF-666-4-Wt-rep_7


title: Tongue 016 LN

source_name: LN


title: MEF-780-8-Ts13-rep_3


title: MEF-780-7-Wt-rep_6


title: MEF-89-5-Wt-rep_3


title: MEF-89-4-Ts16-rep_3

source_name: Mouse Embryo Fibroblast (MEF) with 3 copies of chromosome 16

tag: MEFs grown in DMEM, 10%FCS, 5mM Glutamine, Pen/Strep in humidified chamber at 37Deg C  For 2 Passages with 3 copies of chromosome 16


title: MEF-780-1-Wt-rep_5


title: MEF-89-2-Ts16-rep_1


title: MEF-92-4-Wt-rep_2


title: MEF-776-2-Wt-rep_4


title: MEF-780-2-Ts13-rep_2


title: MEF-92-5-Ts16-rep_2


title: MEF-89-1-Wt-rep_1


title: MIG-2

status: Public on Nov 04 2008

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

country: Canada

institute: Bioinfo

description: bone marrow cells 5 days after 5-FU treatment infected with GFP-control retrovirus, two days later re-sorted for GFP+ cells and cultured for 14 days in cytokines supportive of lymphoid progenitor growth

hyb_protocol: 3.75 micrograms of biotinylated material was hybridized according to the standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol

data_processing: RMA background correction and quantile normalization done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/) which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al Biostatistics (2003).

source_name: MIG-GFP-infected 5-FU BM

label_protocol: 20 nanograms of total RNA was amplified and processed to produce biotinylated cDNA targets using the NuGen Ovation Biotin labeling system.

extract_protocol: Trizol extraction following manufacturer's protocol.

tag: cell type

value: control

tag: Mll-AF4stop knock-in mice


title: ALL#17

description: purified pre B-lymphocytes (B220+ CD43- IgM- IgD-) from bone marrow of a leukemic mouse

source_name: B220+ CD43- IgM- IgD-

value: leukemic preB


title: MEF-776-1-Ts13-rep_1


title: Cre-1

description: bone marrow cells 5 days after 5-FU treatment infected with Cre-GFP retrovirus, two days later re-sorted for GFP+ cells and cultured for 14 days in cytokines supportive of lymphoid progenitor growth

source_name: Cre-GFP-infected 5-FU BM

value: Cre-GFP


title: ALL#15


title: Cre-2


title: ALL#270

description: purified pre B-lymphocytes (B220+ CD43- IgM- IgD-) from bone marrow of a mouse leukemic after pIpC treatment

tag: Mll-AF4stop x Mx1Cre


title: pre-B4

description: purified pre B-lymphocytes (B220+ CD43- IgM- IgD-) from adult mouse bone marrow

value: normal preB


title: MIG-1


title: ALL#A46


title: pre-B3


title: pre-B1


title: mature-B1

description: purified mature B-lymphocytes (B220+ CD43- IgM+ IgD+) from adult mouse bone marrow

source_name: B220+ CD43- IgM+ IgD+

value: normal mature B


title: pre-B2


title: pro-B3

description: purified pro B-lymphocytes (B220+ CD43+ IgM- IgD-) from adult mouse bone marrow

source_name: B220+ CD43+ IgM- IgD-

value: normal proB


title: ALL#227


title: mature-B2


title: immature-B2

description: purified immature B-lymphocytes (B220+ CD43- IgM+ IgD-) from adult mouse bone marrow

source_name: B220+ CD43- IgM+ IgD-

value: normal immature B


title: pro-B2


title: mature-B3


title: immature-B3


title: pro-B1


title: ALL#228


title: ALL#226


title: immature-B1


title: ALL#224


title: ALL#A1507


title: ALL#A1322


title: ALL#153


title: ALL#122


title: ALL#A992


title: ALL#154


title: ALL#117


title: immature-B4


title: pre-B7


title: pre-B6


title: ALL#116

description: purified pre-B cells from Mll-AF4stop knock-in mouse bone marrow


title: pro-B6


title: immature-B5


title: immature-B6


title: pro-B5


title: pre-B5


title: pre-B8


title: cecal tumor, biological replicate 2

status: Public on Oct 24 2008

first: Dmitriy

last: Sonkin

address: 250 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research

description: Gene expression data from cecal tumor.

hyb_protocol: Affymetrix protocol

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Model 3000 7G scanner with autoloader

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

source_name: cecal tumor, biological replicate 2

label_protocol: Affymetrix protocol

extract_protocol: Duodenal mouse tumors (including tumor tissue arising from the pyloris) and cecal tumors were excised with the aid of a Zeiss Stemi SV6 dissecting microscope, and immediately frozen in liquid nitrogen. RNA was extracted from three duodenal and three cecal tumors from six different individual mice, and was purified by using Qiagen RNeasy Kits, and analyzed at the Harvard Partners Center for Genetics and Genomics Microarray Facility. RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100.

tag: cecal tumor


title: pro-B4


title: duodenal tumor, biological replicate 2

description: Gene expression data from duodenal tumor.

source_name: duodenal tumor, biological replicate 2

tag: duodenal tumor


title: duodenal tumor, biological replicate 1

source_name: duodenal tumor, biological replicate 1


title: cecal tumor, biological replicate 3

description: Gene expression data from cecal tumor.

source_name: cecal tumor, biological replicate 3


title: Lung_NiO_1month

status: Public on Oct 23 2008

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Label, hybridization, and scan protocols were performed according to the Agilent manufacturer’s instructions.

hyb_protocol: The hybridization was performed according to the Agilent manufacturer’s instructions.

scan_protocol: Hybridized microarray slides were washed according to the manufacturer’s instructions, and were scanned with an Agilent DNA Microarray Scanner (#G2565BA, Agilent Technologies, Santa Clara, CA) at 5 micron resolution. The scanned images were analyzed numerically using the Agilent Feature Extraction Software version 9.5.3.1.

data_processing:
Normalized data were analyzed using GeneSpring GX version 10.0.1 software (Agilent Technologies, Santa Clara, CA).
Threshold: 1.0
Logbase: 2
Technology: Agilent.SingleColor.14879
Normalization: Shift to 50 percentile

organism: Rattus norvegicus

source_name: Lung, at 1month after inhalation exposure, NiO group (n=4)

label_protocol: cRNA labeled with fluorescent Cyanine 3-CTP was used for hybridization onto the 4 X 44K Whole Rat Genome Oligo Multiplex Microarray slides (#G4131F, Agilent Technologies, Santa Clara, CA) containing approximately 41,000 oligonucleotide probes.

extract_protocol: The right lungs were homogenized with a Tissue Ruptor (Qiagen, Tokyo, Japan). Total RNA from the homogenates was extracted using the RNeasy Midi kit (Qiagen, Tokyo, Japan) following the manufacturer’s instructions. RNA quality and concentration were determined using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA) and a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE).

tag: Male Wistar rats, 9 wk, Whole right lung


title: cecal tumor, biological replicate 1

description: Gene expression data from cecal tumor.

source_name: cecal tumor, biological replicate 1


title: Lung_C60 Fullerene_1month

source_name: Lung, at 1month after inhalation exposure, C60 Fullerene group (n=4)


title: Lung_Control_1month

source_name: Lung, at 1month after inhalation exposure, Fresh air control group (n=4)


title: duodenal tumor, biological replicate 3

source_name: duodenal tumor, biological replicate 3


title: Lung_NiO_3days

source_name: Lung, at 3days after inhalation exposure, NiO group (n=4)