title: 724-1

city: Shanghai

first: Ting

last: Mao

address: 294 Taiyuan Road

country: China

institute: INS, SIBS, CAS

description: Gene expression data from primary hepatocytes expression IRE1aS724A

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45℃, 60rpm on GeneChip mouse 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene array Scanner3000.

data_processing: Normalization was done with the GCRMA package from Bioconductor.

source_name: murine primary hepatocytes overexpressing IRE1aS724A

label_protocol: Biotinylated cRNA were prepared according to manufacturer's instructions (BioArray High Yield RNA Transcript Labeling kit).

growth_protocol: Primary hepatocytes maintained in 37℃, 5%CO2 in HepatoZYME-SFM (Gibco) medium  were infected with the desired adenoviruses Ad-EGFP, Ad-WT, Ad-S724A for 48 hours, or Ad-shCON and Ad-shIRE1a#2 for 72 hours

treatment_protocol: Primary hepatocytes infected with Ad-shCON and Ad-shIRE1a#2 for 72 hours were then treated with glucagon for 4 hours

tag: cells

value: murine primary hepatocytes

tag: genotype/variation

value: IRE1aS724A overexpression

value: no treatment


title: 2hr_control_rep2, R/Bioconductor GC-RMA

status: Public on Aug 31 2011

type: RNA

city: College Station

first: Ginger

last: Carney

state: TX

address: 3258 TAMU

department: Biology

country: USA

institute: Texas A&M University

description:
B1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol using an Affymetrix GCS 3000 7G scanner.

data_processing: All 15 chips were analyzed simultaneously by 4 platforms (5 algorithms): dCHIP, GCOS, Bioconductor, GeneSpring GX 7.3.1. dChip uses a model-based algorithm to estimate expression values. The normalization procedure implemented in dCHIP normalizes all arrays in the analysis against the array with median intensity. This array was analyzed using the PM-MM and PM procedures under default parameters. Expression values were also computed using the recommended settings in GCOS version 1.2. All probesets were scaled using a TGT value of 500, and no normalization was applied (i.e., the normalization factor was 1.0). We also utilized the GC-RMA model-based algorithm in the R-language platform. Bioconductor provided the open source GCRMA and associated packages. In addition, we used the GCRMA model-based algorithm in GeneSpring GX 7.3.1 (Agilent Technologies). Default normalization was the raw intensity value for each probe set on a chip divided by the overall median intensity value for that chip. This “pre-normalized” value was then divided by the median “pre-normalized” value for that specific probe set across all 15 chips in the experiment.

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

source_name: 2hr_male head_control

label_protocol: Standard Affymetrix protocol.

growth_protocol: Stocks were maintained on cornmeal/sugar media at 25oC.

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

treatment_protocol: Virgin males were raised in groups of 20 or fewer flies at 25oC. On day 4, they were transferred to individual vials. On day 5, they were exposed to a virgin female, a cauterized virgin female fly, or no female. 2 hrs after the mated male finished copulating with the female, a male from each group was collected for RNA isolation.

tag: strain

value: isogenized Canton-S

tag: gender

value: male

tag: tissue

value: head

tag: age

value: 5 days

tag: treatment

value: exposure to no female fly

tag: treatment time

value: 2 hours


title: I2G-3

description: Gene expression data from primary hepatocytes knocking down IRE1a and treated with glucagon for 4 hours

organism: Mus musculus

source_name: murine primary hepatocytes knocking down IRE1a, treated with glucagon for 4 hours

value: IRE1a knocking down

value: treated with glucagon for 4 hours


title: 2hr_control_rep5, R/Bioconductor GC-RMA

description:
I1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 2hr_control_rep3, R/Bioconductor GC-RMA

description:
C1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: Flk-1+/Etv2-rep1

city: Kobe

first: Hiroshi

last: Kataoka

state: Hyogo

department: Stem Cell Biology

country: Japan

institute: RIKEN CDB

hyb_protocol: RNA was subsequently fragmented and hybridized to the GeneChip according to manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The raw data were summarized with the RMA algorithm using the R/Bioconductor package (R version 2.8.0, Bioconductor version 2.3).

source_name: Etv2-Venus ES Day5OP9

label_protocol: The 3'IVT Express Kit was used for biotin labeling according to manufacturer's instructions (Affymetrix)

growth_protocol: Etv2-Venus knock-in Het ES cells differentiated to Flk-1+ cells.

extract_protocol: Extract RNA from sorted cells using Micro-elute RNA extraction Kit (Qiagen)

treatment_protocol: Diffrerntiated Flk-1+ cells were separately sorted into  Flk-1+/Etv2- (P3) and  Flk-1+/Etv2+ (P4) populations

tag: cell-line


title: 724-2


title: 2hr_mated_rep3, MAS5.0

description:
C3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

source_name: 2hr_male head_mated

value: exposure to a virgin female fly


title: I2G-2


title: 2hr_courtship_rep3, MAS5.0

description:
C2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

source_name: 2hr_male head_courtship

value: exposure to a cauterized virgin female fly


title: SG-1

description: Gene expression data from primary hepatocytes knocking down control and treated with glucagon for 4 hours

source_name: murine primary hepatocytes knocking down control, treated with glucagon for 4 hours

value: knocking down control


title: 2hr_courtship_rep4, MAS5.0

description:
G2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: SG-2


title: WT-2

description: Gene expression data from primary hepatocytes expression IRE1a

source_name: murine primary hepatocytes overexpressing wildtype IRE1a

value: IRE1a wildtype overexpression


title: SG-3


title: WT-1


title: EGFP-2

description: Gene expression data from primary hepatocytes expression EGFP

source_name: murine primary hepatocytes overexpressing EGFP

value: EGFP overexpression as control


title: 724-3


title: 2hr_courtship_rep1, MAS5.0

description:
A2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: EGFP-1


title: EGFP-3


title: WT-3


title: 2hr_control_rep5, MAS5.0


title: 2hr_courtship_rep2, MAS5.0

description:
B2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 2hr_control_rep2, MAS5.0


title: I2G-1


title: Cortex_NOD_F

city: Chapel Hill

first: Cristina

last: Santos

address: 120 Mason Farm Road

department: Pharmacy (DPET)

institute: UNC-CH

description: pooled tissue (n=3)

hyb_protocol: The resulting cRNA was hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays.

scan_protocol: Standard Affymetrix procedures using the GeneChip 3000 scanner

data_processing: Following normalization with the gcRMA algorithm, expression data were analyzed using ArrayAssist software (Stratagene, La Jolla, CA).

source_name: treatment group (fluoxetine)

label_protocol: RNA samples for three animals from each treatment group were pooled and converted to cDNA and biotinylated cRNA (Enzo kit, Affymetrix, Santa Clara, CA).

growth_protocol: Thirty mouse inbred strains (129S1/SvImJ, A/J, AKR/J, BALB/cJ, BTBRT T(+) tf/J, BUB/BnJ, C3H/HeJ, C57BL/6J, C57BLKS/J, C57BR/cdJ, C58/J, CBA/J, CE/J, DBA/2J, FVB/NJ, I/LnJ, LG/J, LP/J, MA/MyJ, MRL/MpJ, NOD/LtJ, NOR/LtJ, NZB/BlNJ, NZW/LacJ, P/J, PL/J, RIIIS/J, SJL/J, SM/J, and SWR/J)  aged 5-6 weeks old were obtained from The Jackson Laboratory (Bar Harbor, ME). Male mice were kept in polycarbonate cages on a 12-hour light/dark cycle (lights on at 0700h) with access to food and water ad libitum. Following one week of habituation, mice were randomized to either control or treatment group (n=12 male mice per strain per treatment group).

extract_protocol: Brain regions were homogenized in 500 µL of Trizol using a QIAgen TissueLyser at 30 Hz (QIAgen, Valencia, CA). RNA for each animal was isolated by guanidinium thiocyanate-phenol-chloroform extraction and was further purified using the RNAeasy miniprep kit (QIAgen, Valencia, CA) according the manufacturer’s directions. For each strain,

treatment_protocol: Mean water intake for each strain was determined previously by measuring daily water consumption for three weeks (n=12 mice per strain). This information, along with average weight measurements for each strain, was used to determine the amount of fluoxetine required to provide a daily oral dose of 0 or 18 mg/kg per mouse.

value: NOD/LtJ

value: 10-11 week old

value: cortex


title: 2hr_control_rep1, MAS5.0

description:
A1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 2hr_control_rep3, MAS5.0


title: vector cells replicate 3

city: Boston

first: Nina

last: Ilic

state: MA

address: 44 Binney Street

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Gene expression data from cells grown in BEZ235

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133AV2 arrrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneArray Scanner M10

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

organism: Homo sapiens

source_name: HMEC-vector cells grown in 50nM BEZ235 for 72h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Engineered human mammary epithelial cells were grown in HMEC complete media

extract_protocol: Total RNA was extracted using Qiagen Rneasy plus mini kit using standard protcol in the Qiagen QiaCube.

treatment_protocol: Logarithmic cultures of HMEC-derivatives (vector (GFP), p100a(H1047R) (HR), and Enriched cells (E) were treated with 50nM BEZ235 for 72h prior to RNA extraction

tag: cell type

value: engineered mammary epithelial vector cells


title: p100a(H1047R) cells replicate 1

source_name: HMEC-p100a(H1047R) cells grown in 50nM BEZ235 for 72h

value: engineered mammary epithelial p100a(H1047R) cells


title: HMECresistant

type: genomic

description: BEZ235-selected immortal human mammary epithelial cells

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner M10.

data_processing: CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by dChip and model-based expression performed using the PM/MM model and copy number calls generated as compared to Affymetrix normal controls.

molecule: genomic DNA

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: HMECs were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from HMEC cultures using Qiagen DNeasy mini Kit. DNA quality and quantity was assessed using Nanodrop, and agarose gel electrophoresis.


title: 2hr_control_rep4, MAS5.0

description:
G1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: isogenized Canton-S

value: male


title: Cortex_ILN_C

description: pooled tissue (n=3)

source_name: control group (water)

value: I/LnJ


title: Enriched_further

description: BEZ235-selected immortal human mammary epithelial cells containing randomly mutagenized PIK3CA(H1047R)

source_name: enriched HMEC-hTERT-p53DD-p110a(H1047R)


title: 2hr_mated_rep5, dChip PM-MM

description:
I3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: head

value: 5 days


title: Cortex_PJ_F

description: pooled tissue (n=3)

value: P/J


title: Cortex_ILN_F

description: pooled tissue (n=3)


title: p100a(H1047R) cells replicate 3


title: HMEC

description: immortal human mammary epithelial cells

value: immortal human mammary epithelial cells


title: Cortex_NOD_C

description: pooled tissue (n=3)


title: p100a(H1047R) cells replicate 2


title: Enriched

value: BEZ235-selected immortal human mammary epithelial cells containing randomly mutagenized PIK3CA(H1047R)


title: HR1

description: immortal human mammary epithelial cells with oncogenic PIK3CA(H1047R)


title: 2hr_mated_rep4, dChip PM-MM

description:
G3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: exposure to a virgin female fly

value: 2 hours


title: vector cells replicate 2


title: Cortex_LG_F

description: pooled tissue (n=3)

value: LG/J


title: 2hr_mated_rep3, dChip PM-MM


title: HFK cells treated with EpiLife® (EPI) keratinocyte growth medium (control), replicate 3.

city: Bozeman

first: Kate

last: McInnerney

state: MT

address: 109 Lewis Hall

department: Microbiology

institute: Montana State University

description:
Human Foreskin Keratinocytes were isolated at the University of Washington.
control: no S.aureus planktonic or biofilm exposure

hyb_protocol: Labeled and fragmented cRNA was hybridized for 16 hr at 45C to the Affymetrix Human Genome U133A 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix 7G scanner and GCOS version 1.4.

data_processing: Microarray data were analyzed using FlexArray version 1.4.  The Affymetrix CEL files were imported and normalized using GC-RMA.

source_name: Primary human keratinocytes were cultured from newborn foreskin.

label_protocol: Total RNA (500ng) was reverse transcribed, and amplified and biotin-labeled via in vitro transcription using the MessageAmp Premier kit

growth_protocol: Human foreskin kerotinocytes were grown to 90% confluency in six well plates.

extract_protocol: After treatment, the medium was removed and RNA was isolated using an RNeasy minikit following the manufacturer’s instructions for adherent cells.  Extracted RNA was then ethanol precipitated.

treatment_protocol: Cells were then treated with BCM, PCM, or EPI.


title: enriched cells replicate 2

source_name: Enriched HMEC cells grown in 50nM BEZ235 for 72h

value: engineered mammary epithelial cells


title: Cortex_LG_C

description: pooled tissue (n=3)


title: 2hr_mated_rep2, dChip PM-MM

description:
B3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: enriched cells replicate 3


title: vector cells replicate 1


title: Cortex_PJ_C

description: pooled tissue (n=3)


title: HFK cells treated with S.aureus biofilm-conditioned media, replicate 3

description:
Human Foreskin Keratinocytes were isolated at the University of Washington.
S. aureus: Southwest Regional Wound Care isolate # 10948

value: S.aureus biofilm-conditioned media


title: enriched cells replicate 1


title: HFK cells treated with EpiLife® (EPI) keratinocyte growth medium (control), replicate 1.


title: HFK cells treated with S.aureus biofilm-conditioned media, replicate 2

description:
Human Foreskin Keratinocytes were isolated at the University of Washington.
S. aureus: Southwest Regional Wound Care isolate # 10947


title: 2hr_courtship_rep4, dChip PM-MM

description:
G2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: exposure to a cauterized virgin female fly


title: Cortex_MRL_C

description: pooled tissue (n=3)

value: MRL/MpJ

value: 10-11 week old

value: cortex


title: 2hr_courtship_rep3, dChip PM-MM

description:
C2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: isogenized Canton-S


title: 2hr_mated_rep1, dChip PM-MM

description:
A3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: male


title: Cortex_CBA_F

description: pooled tissue (n=3)

value: CBA/J


title: HFK cells treated with EpiLife® (EPI) keratinocyte growth medium (control), replicate 2.


title: HFK cells treated with S.aureus planktonic-conditioned media, replicate 3

description:
Human Foreskin Keratinocytes were isolated at the University of Washington.
S. aureus: Southwest Regional Wound Care isolate # 10945

value: S.aureus planktonic-conditioned media


title: HFK cells treated with S.aureus biofilm-conditioned media, replicate 1

description:
Human Foreskin Keratinocytes were isolated at the University of Washington.
S. aureus: Southwest Regional Wound Care isolate # 10946


title: Cortex_LP_F

description: pooled tissue (n=3)

value: LP/J


title: HFK cells treated with S.aureus planktonic-conditioned media, replicate 2

description:
Human Foreskin Keratinocytes were isolated at the University of Washington.
S. aureus: Southwest Regional Wound Care isolate # 10944


title: Cortex_MRL_F

description: pooled tissue (n=3)


title: 2hr_courtship_rep1, dChip PM-MM

description:
A2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: head

value: 5 days


title: Tissue_model_Epi_200_0.5Gy_625_1125_um_rep4

city: New York

first: Alexandre

last: Mezentsev

state: NY

address: 630 west 168th Street, VC 15-204

department: Dermatology

institute: Columbia University

description: Gene expression in 2.5 Gy-proton irradiated tissue model, 16h postirradiation

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan setting with eXtended dynamic range, Scan area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v1_91_1 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended green Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or Features not Positive and significant were excluded

source_name: human foreskin

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Samples were supplied on ice with overnight delivery and were cultured 24 h prior irradiation and 16 h prior harvesting, postirradiation. Growth medium, NMM-100, was kindly supplied by the manufacturer. Medium was changed every 24h.

extract_protocol: Total RNA was isolated with RNaqueous Kit (Applied Biosystems), tested for spectral characteristics (NanoDrop, Thermo Scientific) and electrophoretically (Bioanalyser 2100, Agilent).

treatment_protocol: Tissues were irradiated with 0 and 0.5Gy of alpha particles

tag: sample type

value: epidermis model


title: 2hr_courtship_rep2, dChip PM-MM

description:
B2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: Tissue_model_Epi_200_0.5Gy_625_1125_um_rep3

description: Gene expression in 0.1 Gy-proton irradiated tissue model, 16h postirradiation


title: Cortex_LP_C

description: pooled tissue (n=3)


title: 2hr_control_rep4, dChip PM-MM

description:
G1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: exposure to no female fly


title: Cortex_CBA_C

description: pooled tissue (n=3)


title: Tissue_model_Epi_200_0.5Gy_125_625_um_rep1

description: Gene expression in 0.1 Gy-proton irradiated tissue model, 4h postirradiation


title: 2hr_control_rep5, dChip PM-MM

description:
I1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: 2 hours


title: Tissue_model_Epi_200_0.5Gy_625_1125_um_rep2

description: Gene expression in 2.5 Gy-proton irradiated tissue model, 4h postirradiation


title: Cortex_MA_F

description: pooled tissue (n=3)

value: MA/MyJ


title: Cortex_SJL_F

description: pooled tissue (n=3)

value: SJL/J


title: Tissue_model_Epi_200_0Gy_125_625_um_rep3


title: Cortex_MA_C

description: pooled tissue (n=3)


title: Cortex_BUB_F

description: pooled tissue (n=3)

value: BUB/BnJ


title: Tissue_model_Epi_200_0.5Gy_125_625_um_rep3


title: 2hr_control_rep2, dChip PM-MM

description:
B1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 2hr_courtship_rep5, dChip PM-MM

description:
I2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: exposure to a cauterized virgin female fly


title: 2hr_control_rep1, dChip PM-MM

description:
A1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: HFK cells treated with S.aureus planktonic-conditioned media, replicate 1

description:
Human Foreskin Keratinocytes were isolated at the University of Washington.
S. aureus: Southwest Regional Wound Care isolate # 10943


title: Tissue_model_Epi_200_0Gy_625_1125_um_rep2


title: Tissue_model_Epi_200_0.5Gy_125_625_um_rep4


title: Tissue_model_Epi_200_0Gy_625_1125_um_rep3

description: Gene expression in 0 Gy-proton irradiated tissue model, 16h postirradiation


title: Cortex_BUB_C

description: pooled tissue (n=3)


title: Tissue_model_Epi_200_0.5Gy_625_1125_um_rep1


title: Cortex_CE_F

description: pooled tissue (n=3)

value: CE/J


title: Cortex_SJL_C

description: pooled tissue (n=3)

value: 10-11 week old


title: Tissue_model_Epi_200_0.5Gy_125_625_um_rep2


title: Tissue_model_Epi_200_0Gy_125_625_um_rep2

description: Gene expression in 0 Gy-proton irradiated tissue model, 4h postirradiation


title: 2hr_control_rep3, dChip PM-MM

description:
C1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: Tissue_model_Epi_200_0Gy_625_1125_um_rep1


title: Tissue_model_Epi_200_0Gy_625_1125_um_rep4


title: Tissue_model_Epi_200_0Gy_125_625_um_rep4


title: Tissue_model_Epi_200_0Gy_125_625_um_rep1


title: Cortex_CE_C

description: pooled tissue (n=3)

value: cortex


title: 2hr_mated_rep3, dChip PM

description:
C3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: isogenized Canton-S

value: exposure to a virgin female fly


title: 2hr_mated_rep1, dChip PM

description:
A3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: male


title: 553-35-206

city: Oxford

first: Jiangting

last: Hu

state: Oxfordshire

address: Headley Way

department: NDCLS

country: United Kingdom

institute: University of Oxford

description: laser captue microdissected tumor epithelial cells RNA for ch1 and URR for ch2 co-hybridisation

hyb_protocol: Dual hybridisation of tumor sample labeled with Cy3 in ch 1 and URR labeled with Cy5 in ch 2 onto cDNA microarray slide.  After hybridization, slides were washed sequential.

scan_protocol: Scanned on a GSI Lumonics 4000 Scanner

data_processing: Images were quantified using and ScanArray software (PerkinElmer Life Science Inc., Boston, Massachusetts). GeneSpring 6.1(Agilent) software was used.

source_name: TN- SCC

label_protocol: 10ug amplified RNA(aRNA) from tumor cells was labeled indirectly with CY3 and the same amout of human reference RNA labeled with CY5

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

tag: smoker

value: yes

tag: Stage

source_name: Universal reference RNA (URR)

value: pool of 10 human carcinoma cell lines, including colon, breast, brain, lung ovarian carcinoma cells as a controlling intra- and inter-experimental variation from Stratagene.


title: 553-33-184

source_name: TN- ADC


title: 2hr_mated_rep5, dChip PM

description:
I3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: head


title: 2hr_mated_rep4, dChip PM

description:
G3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: 5 days


title: Cortex_DBA_F

description: pooled tissue (n=3)


title: 2hr_mated_rep2, dChip PM

description:
B3_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 2hr_courtship_rep5, dChip PM


title: 553-32-153


title: Cortex_AKR_C

description: pooled tissue (n=3)

value: AKR/J


title: 553-34-204


title: Cortex_BR_C

description: pooled tissue (n=3)


title: 553-31-125


title: 2hr_control_rep5, dChip PM

source_name: 2hr_male head_control

value: exposure to no female fly


title: 2hr_courtship_rep1, dChip PM

description:
A2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.

value: 2 hours


title: 2hr_courtship_rep2, dChip PM

description:
B2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 2hr_courtship_rep4, dChip PM

description:
G2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: 2hr_control_rep4, dChip PM

description:
G1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: Cortex_BTB_F

description: pooled tissue (n=3)

value: BTBRT T(+) tf/J


title: Cortex_DBA_C

description: pooled tissue (n=3)


title: 2hr_control_rep3, dChip PM


title: Cortex_BTB_C

description: pooled tissue (n=3)


title: 553-28-8


title: 2hr_courtship_rep3, dChip PM

description:
C2_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: Cortex_NZB_F

description: pooled tissue (n=3)

value: NZB/BlNJ


title: Cortex_AKR_F

description: pooled tissue (n=3)


title: Cortex_C58_F

description: pooled tissue (n=3)


title: 553-41-8L

value: no


title: 553-27-104L


title: 553-29-64


title: 2hr_control_rep1, dChip PM


title: 2hr_control_rep2, dChip PM

description:
B1_121206
Males were randomly pooled in groups of 30 individuals. Heads were removed and used for RNA extraction.


title: Cortex_NZB_C

description: pooled tissue (n=3)


title: 553-30-70


title: Cortex_BR_F

description: pooled tissue (n=3)


title: Cortex_SWR_F

description: pooled tissue (n=3)

value: SWR/J


title: 13689502 - LEC1GR_Dex_1 vs LEC1GR_EtOH_1

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: Identification of LEC1 target genes

hyb_protocol: LEC1GR_EtOH_1 Cy5 / LEC1GR_Dex_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant -  Before induction : solid MS 21°C long day (16h L, 8h D)then during induction: liquid MS, gentle shaking 21°C, long day (16h L, 8h D)

extract_protocol: LEC1GR_EtOH_1:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:EtOH - compound based treatment - compound addition,ethanol:quantity 0.1percent time 8hour . 14 days old seedlings were grown on solid MS and then transferred to liquid MS with the corresponding supplements and incubated under gentle shaking for 8 hours until sampling.

value: EtOH

tag: ecotype

value: LEC1::GR mutant (columbia)

tag: developmental stage

value: boyes 1.02

value: seedling

extract_protocol: LEC1GR_Dex_1:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:Dex - compound based treatment - compound addition,dexamethasone:quantity 30mM . Chemical induction for dex-T-6b gene The plants are treated with 30 (u)mol dexamethasone in 0.01% tween

value: Dex


title: Cortex_C58_C

description: pooled tissue (n=3)

value: male

value: 10-11 week old

value: cortex


title: 534-23-44L

source_name: MT SCC

value: yes

value: pool of 10 human carcinoma cell lines, including colon, breast, brain, lung ovarian carcinoma cells as a controlling intra- and inter-experimental variation from Stratagene.


title: 534-14-31

source_name: TN+ SCC


title: 534-13-27

source_name: TN+ ADC


title: 534-12-252


title: 534-11-131


title: Cortex_SWR_C

description: pooled tissue (n=3)


title: Cortex_SM_C

description: pooled tissue (n=3)

value: SM/J


title: 13689504 - LEC1GR_EtOH_1 vs LEC1GR_Dex_1

description: Identification of LEC1 target genes

hyb_protocol: LEC1GR_Dex_1 Cy5 / LEC1GR_EtOH_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 534-9-59


title: 534-8-54


title: 13689296 - LEC1GR_ABA_1 vs LEC1GR_EtOH_1

description: Identification of LEC1 target genes

hyb_protocol: LEC1GR_EtOH_1 Cy5 / LEC1GR_ABA_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: LEC1GR_ABA_1:10ug. (Qiagen_RNeasy.pdf)

treatment_protocol: Name:ABA - abiotic stress - hormone,abiotic stress,aba:quantity 0.01mM time 1min . Soaking 1 min then incubation 3 hours

value: ABA


title: 13689499 - LEC1GR_ABA_2 vs LEC1GR_EtOH_2

description: Identification of LEC1 target genes

hyb_protocol: LEC1GR_EtOH_2 Cy5 / LEC1GR_ABA_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: LEC1GR_EtOH_2:10ug. (Qiagen_RNeasy.pdf)

extract_protocol: LEC1GR_ABA_2:10ug. (Qiagen_RNeasy.pdf)


title: 534-6-278


title: Cortex_SM_F

description: pooled tissue (n=3)


title: 13689295 - LEC1GR_EtOH_1 vs LEC1GR_ABA_1

description: Identification of LEC1 target genes

hyb_protocol: LEC1GR_ABA_1 Cy5 / LEC1GR_EtOH_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Cortex_PL_F

description: pooled tissue (n=3)

value: PL/J


title: 534-22-252L

value: female


title: Cortex_NZW_F

description: pooled tissue (n=3)

value: NZW/LacJ


title: Cortex_R3_C

description: pooled tissue (n=3)

value: RIIIS/J


title: 13689500 - LEC1GR_EtOH_2 vs LEC1GR_ABA_2

description: Identification of LEC1 target genes

hyb_protocol: LEC1GR_ABA_2 Cy5 / LEC1GR_EtOH_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: kd__MSClike_1

city: St Lucia

first: Darrin

middle: F

last: Taylor

state: Qld

address: Research Rd

department: Genomics and Bioinformatics

country: Australia

institute: Institute for Molecular Bioscience, Uni of Qld

description: Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background corrected and quantile normalized using the Lumi package from Bioconductor(version 2.3, http://www.bioconductor.org)

source_name: kidney derived MSC-like cell

label_protocol: Biotin-labelled aRNA was synthesized with the Illumina RNA Amplification Kit (Ambion, Austin, TX, USA) as per the manufacturer’s instructions.

extract_protocol: RNA extraction was carried out using the Qiagen QIAmp mini kit (without DNAse treatment) as per manufacturer’s instructions.

tag: tissue origin

value: kidney

value: Cells resembling bone marrow MSC


title: Cortex_R3_F

description: pooled tissue (n=3)


title: kd__MSClike_2

description: Replicate 2


title: kd__MSClike_3

description: Replicate 3


title: Cortex_PL_C

description: pooled tissue (n=3)


title: cd_MSClike_4

description: Replicate 4

source_name: cardiac derived MSC-like cell

value: heart


title: kd__MSClike_4

description: Replicate 4


title: 13689292 - LEC1GR_DEXABA_1 vs LEC1GR_EtOH_1

description: Identification of LEC1 target genes

hyb_protocol: LEC1GR_EtOH_1 Cy5 / LEC1GR_DEXABA_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: EtOH

value: LEC1::GR mutant (columbia)

value: boyes 1.02

treatment_protocol: Name:DEX_ABA - compound based treatment - compound addition,dexamethasone 30µm+ abscisic acid10µm:time 8hour . 30µM Dex and 10µM ABA

value: DEX + ABA


title: 13689291 - LEC1GR_EtOH_1 vs LEC1GR_DEXABA_1

description: Identification of LEC1 target genes

hyb_protocol: LEC1GR_DEXABA_1 Cy5 / LEC1GR_EtOH_1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: seedling


title: cd_MSClike_2

description: Replicate 2


title: cd_MSClike_3

description: Replicate 3


title: 534-19-131L

source_name: MT ADC

value: male

value: no


title: 534-18-64L

value: yes

value: pool of 10 human carcinoma cell lines, including colon, breast, brain, lung ovarian carcinoma cells as a controlling intra- and inter-experimental variation from Stratagene.


title: 534-17-54L


title: 13689501 - LEC1GR_Dex_2 vs LEC1GR_EtOH_2

description: Identification of LEC1 target genes

hyb_protocol: LEC1GR_EtOH_2 Cy5 / LEC1GR_Dex_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: LEC1GR_Dex_2:10ug. (Qiagen_RNeasy.pdf)

value: Dex


title: 13689289 - LEC1GR_DEXABA_2 vs LEC1GR_EtOH_2

description: Identification of LEC1 target genes

hyb_protocol: LEC1GR_EtOH_2 Cy5 / LEC1GR_DEXABA_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 534-3-278


title: 13689503 - LEC1GR_EtOH_2 vs LEC1GR_DEXABA_2

description: Identification of LEC1 target genes

hyb_protocol: LEC1GR_DEXABA_2 Cy5 / LEC1GR_EtOH_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MSC_3

description: Replicate 3

source_name: classical (Bone Marrow) derived MSC

value: bone marrow

value: mesenchymal stem cells (MSC)


title: 13697301 - WTEtOH_3 vs WTDex_3

description: Identification of LEC1 target genes

hyb_protocol: WTDex_3 Cy5 / WTEtOH_3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - solid MS, 21°C, long day (16h L, 8hD)before induction then liquid MS, gentle shaking 21°C, long day (16h L, 8hD)during induction

value: boyes 1.02 (boyes et al. plant cell 2001)

value: whole seedling

value: DEX inducible Lec1 transgene

value: DEX

value: EtoH


title: 13689290 - LEC1GR_EtOH_2 vs LEC1GR_Dex_2

description: Identification of LEC1 target genes

hyb_protocol: LEC1GR_Dex_2 Cy5 / LEC1GR_EtOH_2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: EtOH


title: MSC_4

description: Replicate 4


title: Cortex_NZW_C

description: pooled tissue (n=3)

hyb_protocol: The resulting cRNA was hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays.

value: NZW/LacJ

value: 10-11 week old

value: cortex


title: 534-15-44


title: 13689507 - WTDex_3 vs WTEtOH_3

description: Identification of LEC1 target genes

hyb_protocol: WTEtOH_3 Cy5 / WTDex_3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Cortex_FVB_C

description: pooled tissue (n=3)

value: FVB/NJ


title: MSC_2

description: Replicate 2


title: MSC_1

description: Replicate 1


title: IgG 2

city: Irvine

first: Ippei

last: Nagamori

state: CA

address: 2226B GNRF

institute: University of California, Irvine

description: Immunoprecipitated RNA

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.. The labeled samples were individually hybridized onto DNA chip surface, and incubated at 42 ℃ for 16 hours.

scan_protocol: 3D-Gene Scanner 3000 (Toray Industries, Inc.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments). Washed and dried DNA chip in an ozone-removed environment was scanned using a ProScanArray™ microarray scanner. The obtained microarray images were analyzed using the Genepix Pro™ 4.0 software.

data_processing:
F635 Median column as Red signal. The raw data of each spot was globally normalized by adjusting the median signal intensity for each DNA chip to be 30.
The median values of the foreground signal minus the local background were represented as feature intensities. All data obtained from microarray experiments were normalized by a quantile normalization method, and filtered.

source_name: IgG control

label_protocol:
Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..
For each patient, 500 ng of total RNA derived from tumor and non-tumor samples were labeled using miRCURY LNA™ microRNA Power Labeling Kits Hy5

extract_protocol:
Two testes is shared by 18G and 25G needle in 1ml PBS(-). Centrifuge it 1000g at 4degree and discard the sup. The testicular cell pellets were  lysed in 1ml of MVH IP buffer (10mM Trisp pH7.5, 200mM NaCl, 2.5mM MgCl2, 0.5%NP40, 0.1%Triton X100, supplemented with protease inhibitor  cocktail(Roche), 1mM DTT, 5mM NaF, and 40U/ml RNasin) and rock it for 30min at 4degree. Centrifuge it 16,200g for 15min at 4degree and mix the  supernatant and 20microlitter of Protein A dynal beads (Invitrogen) for 1hour at 4degree. Mix 400microlitter of the supernatant and 10microlitter  normal rabbit IgG or 10microlitter of anti-MVH/DDX4 antibody. Rock them for O/N at 4degree. Add 20microlitter of Protein A dynal beads and rock  them for 1hour at 4degree. Wash them by 1ml of MVH IP buffer 5min. repeat wash 4times more, total 5times washes. Co-precipitated RNA was extracted by Trizol.
Tumor and non-tumor tissues were obtained and frozen in liquid nitrogen immediately after hepatic resection, and stored in liquid nitrogen until RNA extraction. Total RNA samples were extracted by a phenol-chloroform RNA extraction method.

value: Testis

tag: antibody

value: normal rabbit IgG

tag: antibody vendor

value: Santa cruz

tag: antibody catalog#


title: Cortex_NOR_F

description: pooled tissue (n=3)

source_name: treatment group (fluoxetine)

tag: strain

value: NOR/LtJ

value: male


title: 9180_ATT

city: Stanford

first: Miao-Chih

last: Tsai

address: 269 Campus Drive, CCSR 2140

institute: Stanford University

description: Postnatal Hepatocytes  derived from TauGFP-AlbCre-R26-lsl-tomato cultured for 12 days and sorted for tdTomato+ cells before RNA extraction.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Hepatocyte

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

growth_protocol: cells grow in standard hepatocyte culturing media or neuronal medium.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: TetO-FUW-based lentiviruses were prepared as previously described with some modification for hepatocytes.

tag: background strain

value: a mixed background C57BL/6;129S

value: Postnatal Hepatocytes


title: Cortex_NOR_C

description: pooled tissue (n=3)

source_name: control group (water)

tag: gender

tag: tissue


title: WCE 2

description: Total RNA

source_name: WCE control


title: cd_MSClike_1

description: Replicate 1

value: heart

value: Cells resembling bone marrow MSC


title: Cortex_C3H_C

description: pooled tissue (n=3)

tag: age


title: WCE 1

description: Total RNA


title: 13689300 - WTEtOH_2 vs WTDex_2

description: Identification of LEC1 target genes

hyb_protocol: WTDex_2 Cy5 / WTEtOH_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: boyes 1.02 (boyes et al. plant cell 2001)

value: whole seedling

value: DEX inducible Lec1 transgene

tag: treatment


title: Cortex_C3H_F

description: pooled tissue (n=3)


title: 9179_BAM_ATT

description: Hep-iN cells (Hepatocytes derived induced neurons) derived from TauGFP-AlbCre-R26-lsl-tomato (13 days after infection with the 3 factors (Ascl1 - Brn2 - Myt1l) double sorted for tdTomato+GFP+ cells before RNA extraction.

source_name: Hepatocyte with BAM


title: 9178_BAM

description: MEF-iN cells (MEF derived induced neurons) derived from TauGFP embryos 13 days after infection with the 3 factors (Ascl1 -Brn2 - Myt1l) and sorted for GFP+ cells before RNA extraction.

source_name: MEFs with BAM


title: post_IRI_3

city: Baltimore

first: Dmitry

middle: N

last: Grigoryev

state: MD

institute: JHU

description: replicate 3

hyb_protocol: Not Applicable

scan_protocol: Applied Biosystem 7300 Real Time PCR System.  ABI instrument settings include setting reporter dye as “SYBR”, passive reference is “ROX”.  Delete UNG Activation, and add Dissociation Stage

data_processing: Relative gene expressions were calculated by using the 2-  Ct method, in which Ct indicates cycle threshold, the fractional cycle number where the fluorescent signal reaches detection threshold 15.  The normalized ΔCt value of each sample is calculated using up to a total of 5 endogenous control genes (18S rRNA, HPRT1, RPL13A, GAPDH, and ACTB). Fold change values are presented as average fold change = 2-(average   Ct) for genes in treated relative to control samples (see GSE23747 supplementary file for normalized fold-change data).

label: SYBR Green/ROX

source_name: mouse kidney CD3+ T-cells

label_protocol: Reverse transcription was performed on total RNA isolated from CD3 (+) T cells extracted from kidneys and processed with Applied Biosystems (Foster City, CA). High-Capacity cDNA Archive kit first-strand synthesis system for RT-PCR was used according to the manufacturer's protocol.  QRT-PCR (Quantitative real time-polymerase chain reaction) was performed using the RT2 ProfilerTM PCR Array from SuperArray (SABiosciences, Gaithersburg, MD).   RT² Profiler™ PCR Arrays are designed for relative quantitative QRT-PCR based on SybrGreen detection and performed on a one sample/one plate 96-well

extract_protocol: Total RNA from CD3 (+) T cells population was extracted using the Trizol Reagent method (Invitrogen, Carlsbad, CA). The quality of total RNA samples was assessed using nanodrop (Thermoscientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: 6-8-wk-old male

value: isolated CD3+ T-cells


title: Cortex_FVB_F

description: pooled tissue (n=3)

value: 10-11 week old


title: Cortex_BLKS_C

description: pooled tissue (n=3)

value: cortex


title: IgG 1

description: Immunoprecipitated RNA


title: 9177_BAM

value: MEF-iN cells (MEF derived induced neurons)


title: 13689301 - WTDex_2 vs WTEtOH_2

description: Identification of LEC1 target genes

hyb_protocol: WTEtOH_2 Cy5 / WTDex_2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: EtoH

value: DEX


title: Cortex_BLKS_F

description: pooled tissue (n=3)


title: post_IRI_4

description: replicate 4


title: Control_4

description: replicate 4


title: Control_3

description: replicate 3


title: Cortex_B6_F

description: pooled tissue (n=3)


title: Control_2

description: replicate 2


title: MVH 1

description: Immunoprecipitated RNA

source_name: MVH

value: Testis

value: anti-MVH antibody

value: Abcam


title: 9171_MEF

description: uninfected MEF passage 3

source_name: MEFs

value: a mixed background C57BL/6;129S

value: uninfected MEF


title: 9172_MEF

description: uninfected MEF passage 3


title: Cortex_BLB_C

description: pooled tissue (n=3)

value: BALB/cJ

value: male


title: Cortex_B6_C

description: pooled tissue (n=3)


title: Cortex_BLB_F

description: pooled tissue (n=3)


title: Control_1

description: replicate 1


title: 9176_neuron

description: Postnatal cortical neurons derived from TauGFP mice, cultured for 13 days and sorted for GFP+ cells before RNA extraction

source_name: cortical neurons

value: cortical neuron


title: Cortex_AJ_C

description: pooled tissue (n=3)

value: A/J


title: Cortex_129_F

description: pooled tissue (n=3)


title: Cortex_AJ_F

description: pooled tissue (n=3)


title: Cortex_129_C

description: pooled tissue (n=3)


title: G3 rep1

city: Charlottesville

first: Carol

middle: A

last: Gilchrist

state: VA

address: Dept. of Medicine/Division of Infectious Diseases, Building MR4, Rm 2126,PO Box 801365

department: Medicine

institute: University of Virginia

description: Gene expression data from E. histolytica G3 transfectants

hyb_protocol: The standard protocol for hybridization of eukaryotic mRNA to Affymetrix arrays was followed as described: (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

scan_protocol: The arrays were scanned with an Affymetrix Gene Chip scanner 7G and report files were generated to determine the percentage of present calls of each array.  The detection calls (present, marginal, absent) for each probe set were obtained using the GCOS system (http://www.affymetrix.com/products/software/specific/gcos.affx).

data_processing: Analysis was performed using the Partek® Genomics Suite (Partek Inc., St. Louis, Missouri 63141) software. CEL files (containing raw expression measurements) were imported to Partek GS. The data was preprocessed and normalized using the RMA (Robust Multichip Average) algorithm (Irizarryet al 2003). Quality control of the normalized data was performed using PCA (Principal component analysis) and hierarchical clustering. To identify differentially expressed genes one way ANOVA analysis of variance was applied. FDR (false discovery rate) was used to correct for multiple comparisons (Benjamini Y, Hochberg Y. 1995).

organism: Entamoeba histolytica

label_protocol: Two micrograms of total RNA was used for cDNA and subsequent biotinalated cRNA synthesis  (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

growth_protocol: Trophozoites of E. histolytica strain HM-1:IMSS and of the plasmid-less, amoebapore gene-silenced clone G3 (Bracha et al 2006)  were grown at 37C in TYI-S-33 medium (Diamond et al 1978).

extract_protocol: Total RNA was prepared using the RNA isolation kit TRI Reagent (Sigma). For the fractionation of RNA into nuclear RNA and RNA bound to the polysomal fraction, exponentially growing trophozoites were harvested and washed in cold PBS. The cells were resuspended (107 cell/ml) in a lysis solution containing 1% NP-40 (Nonidet P-40 nonionic detergent) in 35 mM Hepes buffer (4-(2-hydroxy-ethyl)-I-piperazine,10 mM MgCl2, 24 mM KCl, 0.2 mM PMSF, and 5 mM b-mercaptoethanol, with occasional mixing. The lysate was sedimented for 5 min (500 x g, 4°C), The pellet, containing the nuclei  (referred as the nuclear fraction) was washed once more in the same lysis buffer and RNA was prepared with the TRI Reagent kit as above.. The supernatant, containing the polyribosomal fraction was sedimented for 2 h at 33,000 rpm in a fixed angle rotor Ti50 (Beckman, Palo Alto, CA, USA) and the pellet containing the polysome–bound mRNA was resuspended in TE buffer (10 mM TrisHCl/l mM EDTA pH 7.5) and extracted with a mixture of phenol/chloroform (1:l) prewarmed to 65’C. The RNA was precipitated with a solution of sodium acetate (pH 6.0, 0.3 M) in 70% ethanol (Petter et al 1994) Quality control of RNA samples was preformed by use of the Agilent Bioanalyser Nano Assay.

treatment_protocol: Transfection of trophozoites was performed as previously described (Alon et al 1997), and the amoebae were grown in the presence of the neomycin derivative G418 (Bracha et al 2006).

value: trophozoites


title: HM-1:IMSS rep2

description: Gene expression data from HM-1:IMSS


title: HM-1:IMSS rep1

description: Gene expression data from HM-1:IMSS


title: ESC shRNA linc1422_hp5s1_R2 (batch 3)

status: Public on Aug 30 2011

city: Cambridge

first: Mitchell

last: Guttman

address: 7 Cambridge Center

institute: Broad Institute

hyb_protocol: We mixed 600ng of cRNA with blocking agent and fragmentation buffer (Agilent, 5190 0404) and fragmented for 30 minutes in the dark at 60°C.  We added 2x Hybridization Buffer to each sample and loaded 40ul onto an 8-pack Hybridization gasket.  We placed the microarray slides on top, sealed in the Hybridization Chamber, and incubated for 18 hours at 65°C.  We washed the slides for 1 minute in room temperature GE Wash Buffer 1 and then for 1 minute in 37°C GE Wash Buffer 2 (Agilent 5188 5327, no triton addition).  We scanned the microarrays using an Agilent Scanner C (G2565CA) using the following settings: Dye Channel = Red&Green, Scan Region = ScanArea (61x21.6mm), Scan Resolution = 3 m. We prepared all of the samples simultaneously using homogenous master mixes to limit variability. Fragmentation and hybridization was staggered over time in batches of 3 to 4 slides (24 to 32 samples).

scan_protocol: Each array was processed and data extracted using the Agilent feature extraction software (G4462AA, Version 10.7.3).

data_processing: Gene expression values were determined using the gProcessedSignal intensity values. Probes were flagged if they were not detectable well above background or had an expression level lower than the lowest detectable spike-in control value. The values were floored across all samples by taking the maximum of the minimum non-flagged values across all experiments. Any value less than this maximum value were set to the maximum. To normalize expression values across arrays, we performed quantile normalization as previously described. Briefly, we ranked each array from lowest to highest expression. For each rank, we computed the average expression and each experiment with this value at the associated rank. For each probe, we computed the difference between the second smallest expression value and the second largest expression value. If this difference was less than 2, we filtered the probe. This metric was chosen to eliminate bias due to single sample outliers.

source_name: mESC shRNA treated 4 days

label_protocol: Using Agilent’s One-Color Quick Amp Labelling kit (5190-0442), we amplified and labelled total RNA for hybridization to prototype mouse lincRNA arrays (G4140-90040) according to manufacturer’s instructions with a few variations. The cRNA samples were prepared by diluting 200ng of RNA in 8.3ul water and adding positive control one-color RNA spike-in mix (Agilent, 5188-5282) that was diluted serially 1:20, then 1:25 and finally 1:10. We annealed the T7 promoter primer from the kit by incubating at 65°C for 10 minutes.  We prepared the cDNA master mix and added to the annealed RNA and incubated at 40°C for 2 hours, followed by 65°C for 15 minutes.  We prepared the cRNA transcription master mix and added it to the cDNA and incubated at 40°C for 2 hours protected from light. We purified the labeled cRNA using Qiagen’s RNeasy 96-well columns (Qiagen, 74181) by adding 350ul of Qiagen RLT (without BME) to the cRNA followed by the addition of 250ul of 95% ethanol before applying to the plate column.  After a 4 minute spin at 6000RPM, we washed the columns 3 times with 800ul buffer RPE. We dried the columns by spinning for 10 minutes and eluted the cRNA with 50ul of water.  We measured the cRNA yield and dye incorporation using the Nanodrop 8000 Microarray measurement setting.

growth_protocol: V6.5 ES cells were plated at a density of 5000 cells/well in 100ul mES media onto pre-gelatinized 96-well dishes (VWR; BD356689).  Cells were infected with 5ul of a lentiviral shRNA stock and incubated at 37°C for 30 minutes.  Puromycin resistant DR4 MEFs (GlobalStem; GSC-6004G) were then added to the plates at a density of ~6000/well and incubated overnight at 37°C, 5% CO2.  After 24 hours, all media was removed from the cells and replaced with media containing 1ug/mL puromycin.  Media was then changed every other day with fresh media containing 1ug/mL puromycin.

extract_protocol: ES cells were infected and lysed at day 4 with 150ul of Qiagen’s RLT buffer and 3 replicates of each virus plate were pooled for RNA extraction using Qiagen’s RNeasy 96-well columns (74181).  RNA extraction was completed following Qiagen’s RNeasy 96-well protocol with the following modifications: 450ul of 70% ethanol was added to 450ul total lysate prior to the first spin.  An additional RPE wash was added to the protocol, for a total of 3 RPE washes.

tag: cell line

tag: knockdown

value: shRNA knockdown of linc1422


title: ESC shRNA rfp_403s1c1_R2 (batch 3)

treatment_protocol: Cells were infected with 5ul of a lentiviral shRNA stock and incubated at 37°C for 30 minutes.

value: shRNA knockdown of RFP


title: G3 rep2


title: ESC shRNA linc1427_hp1s1_R2 (batch 3)

value: shRNA knockdown of linc1427


title: ESC shRNA linc1547_hp4s1_R3 (batch 3)

value: shRNA knockdown of linc1547


title: ESC shRNA LKO18bp_R1 (batch 3)

value: shRNA knockdown of pLKO


title: ESC shRNA LKO18bp_R2 (batch 3)


title: ESC shRNA linc1427_hp1s1_R1 (batch 3)


title: ESC shRNA rfp_403s1c1_R1 (batch 3)


title: ESC shRNA LKO18bp_R3 (batch 3)


title: ESC shRNA promegaLuc_164s1c1_R1 (batch 3)

value: shRNA knockdown of Luciferase


title: ESC shRNA rfp_513s1c1_R1 (batch 3)


title: ESC shRNA promegaLuc_743s1c1_R2 (batch 3)


title: ESC shRNA promegaLuc_743s1c1_R1 (batch 3)


title: ESC shRNA linc1422_hp5s2_R3 (batch 3)


title: ESC shRNA linc1547_hp4s1_R2 (batch 3)


title: ESC shRNA rfp_403s1c1_R3 (batch 3)


title: ESC shRNA linc1547_hp4s1_R1 (batch 3)


title: ESC shRNA linc1427_hp1s1_R3 (batch 3)


title: ESC shRNA linc1422_hp5s1_R1 (batch 3)


title: ESC shRNA linc1406_hp5s1_R1 (batch 3)

value: shRNA knockdown of linc1406


title: post_IRI_1

description: replicate 1

value: 6-8-wk-old male

tag: cell type

value: isolated CD3+ T-cells


title: ESC shRNA linc1406_hp5s1_R2 (batch 3)


title: ESC shRNA linc1393_hp2s1_R2 (batch 3)

value: shRNA knockdown of linc1393


title: ESC shRNA linc1393_hp2s1_R3 (batch 3)


title: post_IRI_2

description: replicate 2


title: ESC shRNA linc1393_hp2s1_R1 (batch 3)


title: ESC shRNA linc1354_hp4s1_R3 (batch 3)

value: shRNA knockdown of linc1354


title: ESC shRNA linc1354_hp4s1_R1 (batch 3)


title: ESC shRNA lacZ_1339s1c1_R2 (batch 3)

value: shRNA knockdown of LacZ


title: ESC shRNA lacZ_1935s1c1_R4 (batch 3)


title: MVH 2

description: Immunoprecipitated RNA

value: Testis

value: anti-MVH antibody

value: Abcam


title: ESC shRNA linc1257_hp5s1_R1 (batch 3)

value: shRNA knockdown of linc1257


title: ESC shRNA linc1317_hp4s1_R3 (batch 3)

value: shRNA knockdown of linc1317


title: ESC shRNA linc1354_hp4s1_R2 (batch 3)


title: ESC shRNA GFP-437_R2 (batch 3)

value: shRNA knockdown of GFP


title: ESC shRNA linc1251_hp5s1_R2 (batch 3)

value: shRNA knockdown of linc1251


title: ESC shRNA linc1317_hp4s1_R2 (batch 3)


title: ESC shRNA linc1257_hp5s1_R2 (batch 3)


title: ESC shRNA linc1317_hp4s1_R4 (batch 3)


title: ESC shRNA lacZ_1339s1c1_R3 (batch 3)


title: ESC shRNA linc1251_hp5s1_R1 (batch 3)


title: ESC shRNA clonetechGfp_684s1c1_R1 (batch 3)


title: ESC shRNA linc1317_hp4s1_R1 (batch 3)


title: ESC shRNA rfp_402s1c1_R1 (batch 2)

value: shRNA knockdown of RFP


title: ESC shRNA GFP-437_R1 (batch 3)


title: ESC shRNA lacZ_1339s1c1_R1 (batch 3)


title: ESC shRNA clonetechGfp_438s1c1_R1 (batch 3)


title: ESC shRNA XM_132755_R1 (batch 2)

value: shRNA knockdown of XM_132755


title: ESC shRNA XM_132755_R2 (batch 2)


title: ESC shRNA rfp_513s1c1_R1 (batch 2)


title: ESC shRNA clonetechGfp_684s1c1_R2 (batch 3)


title: ESC shRNA promegaLuc_743s1c1_R1 (batch 2)


title: ESC shRNA NM_013633_R1 (batch 2)

value: shRNA knockdown of NM_013633


title: ESC shRNA promegaLuc_601s1c1_R1 (batch 2)

value: shRNA knockdown of Luciferase


title: ESC shRNA NM_013633_R2 (batch 2)


title: ESC shRNA promegaLuc_164s1c1_R1 (batch 2)


title: ESC shRNA linc1627_1.1-355s21c1_R1 (batch 2)

value: shRNA knockdown of linc1627


title: ESC shRNA linc1626_1.1-533s21c1_R2 (batch 2)

value: shRNA knockdown of linc1626


title: ESC shRNA linc1627_1.1-355s21c1_R2 (batch 2)


title: ESC shRNA linc1621_1.1-570s21c1_R1 (batch 2)

value: shRNA knockdown of linc1621


title: ESC shRNA linc1596_1.1-167s21c1_R2 (batch 2)

value: shRNA knockdown of linc1596


title: ESC shRNA rfp_283s1c1_R1 (batch 2)


title: ESC shRNA linc1607_1.1-210s21c1_R1 (batch 2)

value: shRNA knockdown of linc1607


title: ESC shRNA linc1607_1.1-210s21c1_R2 (batch 2)


title: ESC shRNA linc1626_1.1-533s21c1_R1 (batch 2)


title: ESC shRNA linc1621_1.1-570s21c1_R2 (batch 2)


title: ESC shRNA linc1600_1.1-73s21c1_R1 (batch 2)

value: shRNA knockdown of linc1600


title: ESC shRNA linc1596_1.1-167s21c1_R1 (batch 2)


title: ESC shRNA linc1536_1.1-1584s21c1_R1 (batch 2)

value: shRNA knockdown of linc1536


title: ESC shRNA linc1506_1.1-189s21c1_R2 (batch 2)

value: shRNA knockdown of linc1506


title: ESC shRNA linc1592_2.1-561s21c1_R1 (batch 2)

value: shRNA knockdown of linc1592


title: ESC shRNA linc1503_1.1-698s21c1_R1 (batch 2)

value: shRNA knockdown of linc1503


title: ESC shRNA linc1608_1.1-69s21c1_R1 (batch 2)

value: shRNA knockdown of linc1608


title: ESC shRNA linc1505_1.1-311s21c1_R2 (batch 2)

value: shRNA knockdown of linc1505


title: ESC shRNA linc1484_2.1-92s21c1_R1 (batch 2)

value: shRNA knockdown of linc1484


title: ESC shRNA linc1477_1.1-121s21c1_R1 (batch 2)

value: shRNA knockdown of linc1477


title: ESC shRNA linc1506_1.1-189s21c1_R1 (batch 2)


title: ESC shRNA linc1405_1.1-5329s21c1_R2 (batch 2)

value: shRNA knockdown of linc1405


title: ESC shRNA linc1484_2.1-92s21c1_R2 (batch 2)


title: ESC shRNA linc1448_1.1-297s21c1_R2 (batch 2)

value: shRNA knockdown of linc1448


title: ESC shRNA linc1505_1.1-311s21c1_R1 (batch 2)


title: ESC shRNA linc1356_1.1-488s21c1_R2 (batch 2)

value: shRNA knockdown of linc1356


title: ESC shRNA linc1503_1.1-698s21c1_R2 (batch 2)


title: ESC shRNA linc1477_1.1-121s21c1_R2 (batch 2)


title: ESC shRNA linc1296_1.1-524s21c1_R1 (batch 2)

value: shRNA knockdown of linc1296


title: ESC shRNA linc1327_1.1-221s21c1_R2 (batch 2)

value: shRNA knockdown of linc1327


title: ESC shRNA linc1300_1.1-266s21c1_R2 (batch 2)

value: shRNA knockdown of linc1300


title: ESC shRNA linc1405_1.1-5329s21c1_R1 (batch 2)


title: ESC shRNA linc1359_1.1-639s21c1_R1 (batch 2)

value: shRNA knockdown of linc1359


title: ESC shRNA linc1356_1.1-488s21c1_R1 (batch 2)


title: ESC shRNA linc1359_1.1-639s21c1_R2 (batch 2)


title: ESC shRNA linc1337_1.1-363s21c1_R2 (batch 2)

value: shRNA knockdown of linc1337


title: ESC shRNA linc1338_1.1-101s21c1_R1 (batch 2)

value: shRNA knockdown of linc1338


title: ESC shRNA linc1448_1.1-297s21c1_R1 (batch 2)


title: ESC shRNA linc1327_1.1-221s21c1_R1 (batch 2)


title: ESC shRNA linc1337_1.1-363s21c1_R1 (batch 2)


title: ESC shRNA linc1296_1.1-524s21c1_R2 (batch 2)


title: ESC shRNA linc1338_1.1-101s21c1_R2 (batch 2)


title: ESC shRNA linc1300_1.1-266s21c1_R1 (batch 2)


title: ESC shRNA linc1256_1.1-745s21c1_R2 (batch 2)

value: shRNA knockdown of linc1256


title: ESC shRNA linc1282_1.1-223s21c1_R2 (batch 2)

value: shRNA knockdown of linc1282


title: ESC shRNA linc1267_1.1-93s21c1_R1 (batch 2)

value: shRNA knockdown of linc1267


title: ESC shRNA linc1289_2.1-89s21c1_R1 (batch 2)

value: shRNA knockdown of linc1289


title: ESC shRNA linc1282_1.1-223s21c1_R1 (batch 2)


title: ESC shRNA linc1267_1.1-93s21c1_R2 (batch 2)


title: ESC shRNA linc1260_1.1-116s21c1_R2 (batch 2)

value: shRNA knockdown of linc1260


title: ESC shRNA linc1252_2.1-3022s21c1_R2 (batch 2)

value: shRNA knockdown of linc1252


title: ESC shRNA linc1252_2.1-3022s21c1_R1 (batch 2)


title: ESC shRNA linc1260_1.1-116s21c1_R1 (batch 2)


title: ESC shRNA clonetechGfp_449s1c1_R1 (batch 2)

value: shRNA knockdown of GFP


title: ESC shRNA linc1281_1.1-800s21c1_R1 (batch 2)

value: shRNA knockdown of linc1281


title: ESC shRNA linc1245_3.1-836s21c1_R1 (batch 2)

value: shRNA knockdown of linc1245


title: ESC shRNA clonetechGfp_197s1c1_R1 (batch 2)


title: ESC shRNA lacZ_2082s1c1_R1 (batch 2)

value: shRNA knockdown of LacZ


title: ESC shRNA XM_132755.3_R1 (batch1)

value: shRNA knockdown of XM_132755


title: ESC shRNA rfp_66_R1 (batch1)

value: shRNA knockdown of RFP


title: ESC shRNA clonetechGfp_477s1c1_R1 (batch 2)


title: ESC shRNA rfp_402_R1 (batch1)


title: ESC shRNA rfp_403_R1 (batch1)


title: ESC shRNA lacZ_1650s1c1_R1 (batch 2)


title: ESC shRNA rfp_283_R1 (batch1)


title: ESC shRNA promegaLuc_743_R1 (batch1)

value: shRNA knockdown of Luciferase


title: ESC shRNA rfp_402_R2 (batch1)


title: ESC shRNA rfp_513_R1 (batch1)


title: ESC shRNA XM_132755.3_R2 (batch1)


title: ESC shRNA linc1289_2.1-89s21c1_R2 (batch 2)


title: ESC shRNA linc1274_1.1-608s21c1_R1 (batch 2)

value: shRNA knockdown of linc1274


title: ESC shRNA promegaLuc_168_R1 (batch1)


title: ESC shRNA promegaLuc_164_R1 (batch1)


title: ESC shRNA linc1256_1.1-745s21c1_R1 (batch 2)


title: ESC shRNA promegaLuc_601_R1 (batch1)


title: ESC shRNA pLKO_R1 (batch1)

value: shRNA knockdown of pLKO


title: ESC shRNA pLKO_R2 (batch1)


title: ESC shRNA pLKO_R5 (batch1)


title: ESC shRNA pLKO_R3 (batch1)


title: ESC shRNA NM_201396.1_R2 (batch1)

value: shRNA knockdown of NM_201396


title: ESC shRNA promegaLuc_160_R2 (batch1)


title: ESC shRNA NM_172517.1_R2 (batch1)

value: shRNA knockdown of NM_172517


title: ESC shRNA NM_172517.1_R1 (batch1)


title: ESC shRNA NM_146176.1_R2 (batch1)

value: shRNA knockdown of NM_146176


title: ESC shRNA NM_028610.1_R2 (batch1)

value: shRNA knockdown of NM_028610


title: ESC shRNA NM_146176.1_R1 (batch1)


title: ESC shRNA NM_201396.1_R1 (batch1)


title: ESC shRNA NM_199196.1_R2 (batch1)

value: shRNA knockdown of NM_199196


title: ESC shRNA NM_026570.1_R2 (batch1)

value: shRNA knockdown of NM_026570


title: ESC shRNA NM_030241.2_R2 (batch1)

value: shRNA knockdown of NM_030241


title: ESC shRNA NM_030241.2_R1 (batch1)


title: ESC shRNA NM_028610.1_R1 (batch1)


title: ESC shRNA NM_145830.1_R2 (batch1)

value: shRNA knockdown of NM_145830


title: ESC shRNA NM_029337.1_R1 (batch1)

value: shRNA knockdown of NM_029337


title: ESC shRNA NM_173441.1_R1 (batch1)

value: shRNA knockdown of NM_173441


title: ESC shRNA pLKO_R4 (batch1)


title: ESC shRNA NM_145830.1_R1 (batch1)


title: ESC shRNA NM_029337.1_R2 (batch1)


title: ESC shRNA NM_199196.1_R1 (batch1)


title: ESC shRNA NM_026570.1_R1 (batch1)


title: ESC shRNA NM_022724.2_R2 (batch1)

value: shRNA knockdown of NM_022724


title: ESC shRNA NM_021878.2_R2 (batch1)

value: shRNA knockdown of NM_021878


title: ESC shRNA NM_021876.1_R2 (batch1)

value: shRNA knockdown of NM_021876


title: ESC shRNA NM_021876.1_R1 (batch1)


title: ESC shRNA NM_022724.2_R1 (batch1)


title: ESC shRNA NM_021531.1_R1 (batch1)

value: shRNA knockdown of NM_021531


title: ESC shRNA NM_021878.2_R1 (batch1)


title: ESC shRNA NM_021513.1_R1 (batch1)

value: shRNA knockdown of NM_021513


title: ESC shRNA NM_021513.1_R2 (batch1)


title: ESC shRNA NM_021531.1_R2 (batch1)


title: ESC shRNA NM_019685.1_R1 (batch1)

value: shRNA knockdown of NM_019685


title: ESC shRNA NM_018877.2_R2 (batch1)

value: shRNA knockdown of NM_018877


title: ESC shRNA NM_013668.2_R2 (batch1)

value: shRNA knockdown of NM_013668


title: ESC shRNA NM_019458.2_R2 (batch1)

value: shRNA knockdown of NM_019458


title: ESC shRNA NM_019448.2_R1 (batch1)

value: shRNA knockdown of NM_019448


title: ESC shRNA NM_013633.1_R1 (batch1)

value: shRNA knockdown of NM_013633


title: ESC shRNA NM_011542.1_R2 (batch1)

value: shRNA knockdown of NM_011542


title: ESC shRNA NM_013633.1_R2 (batch1)


title: ESC shRNA NM_019448.2_R2 (batch1)


title: ESC shRNA NM_013668.2_R1 (batch1)


title: ESC shRNA NM_011934.2_R1 (batch1)

value: shRNA knockdown of NM_011934


title: ESC shRNA NM_013633.1_R3 (batch1)


title: ESC shRNA NM_011640.1_R1 (batch1)

value: shRNA knockdown of NM_011640


title: ESC shRNA NM_019685.1_R2 (batch1)


title: ESC shRNA NM_019458.2_R1 (batch1)


title: ESC shRNA NM_018877.2_R1 (batch1)


title: ESC shRNA NM_011443.2_R2 (batch1)

value: shRNA knockdown of NM_011443


title: ESC shRNA NM_011542.1_R1 (batch1)


title: ESC shRNA NM_011443.2_R1 (batch1)


title: ESC shRNA NM_011486.3_R2 (batch1)

value: shRNA knockdown of NM_011486


title: ESC shRNA NM_011304.1_R2 (batch1)

value: shRNA knockdown of NM_011304


title: ESC shRNA NM_010637.1_R2 (batch1)

value: shRNA knockdown of NM_010637


title: ESC shRNA NM_009337.2_R2 (batch1)

value: shRNA knockdown of NM_009337


title: ESC shRNA NM_008709.2_R1 (batch1)

value: shRNA knockdown of NM_008709


title: ESC shRNA NM_009769.2_R1 (batch1)

value: shRNA knockdown of NM_009769


title: ESC shRNA NM_010637.1_R1 (batch1)


title: ESC shRNA NM_011486.3_R1 (batch1)


title: ESC shRNA NM_010066.2_R2 (batch1)

value: shRNA knockdown of NM_010066


title: ESC shRNA NM_009066.2_R1 (batch1)

value: shRNA knockdown of NM_009066


title: ESC shRNA NM_011304.1_R1 (batch1)


title: ESC shRNA NM_009769.2_R2 (batch1)


title: ESC shRNA NM_008709.2_R2 (batch1)


title: ESC shRNA NM_009556.2_R1 (batch1)

value: shRNA knockdown of NM_009556


title: ESC shRNA NM_009066.2_R2 (batch1)


title: ESC shRNA promegaLuc_160_R1 (batch1)

value: shRNA knockdown of Luciferase


title: ESC shRNA NM_008452.1_R3 (batch1)

value: shRNA knockdown of NM_008452


title: ESC shRNA linc1635_1.1-74_R2 (batch1)

value: shRNA knockdown of linc1635


title: ESC shRNA linc1633_1.1-233_R2 (batch1)

value: shRNA knockdown of linc1633


title: ESC shRNA NM_009337.2_R1 (batch1)


title: ESC shRNA linc1633_1.1-233_R1 (batch1)


title: ESC shRNA linc1634_1.1-480_R1 (batch1)

value: shRNA knockdown of linc1634


title: ESC shRNA NM_007971.1_R1 (batch1)

value: shRNA knockdown of NM_007971


title: ESC shRNA linc1632_1.1-81_R1 (batch1)

value: shRNA knockdown of linc1632


title: ESC shRNA linc1631_1.1-125_R2 (batch1)

value: shRNA knockdown of linc1631


title: ESC shRNA NM_007690.1_R1 (batch1)

value: shRNA knockdown of NM_007690


title: ESC shRNA NM_008452.1_R1 (batch1)


title: ESC shRNA linc1632_1.1-81_R2 (batch1)


title: ESC shRNA linc1630_1.1-287_R2 (batch1)

value: shRNA knockdown of linc1630


title: ESC shRNA linc1631_1.1-125_R1 (batch1)


title: ESC shRNA NM_007690.1_R2 (batch1)


title: ESC shRNA NM_007622.2_R1 (batch1)

value: shRNA knockdown of NM_007622


title: ESC shRNA linc1624_1.1-281_R1 (batch1)

value: shRNA knockdown of linc1624


title: ESC shRNA linc1629_1.1-110_R1 (batch1)

value: shRNA knockdown of linc1629


title: ESC shRNA NM_007624.1_R1 (batch1)

value: shRNA knockdown of NM_007624


title: ESC shRNA NM_008452.1_R2 (batch1)


title: ESC shRNA linc1623_1.1-235_R2 (batch1)

value: shRNA knockdown of linc1623


title: ESC shRNA linc1624_1.1-281_R2 (batch1)


title: ESC shRNA linc1635_1.1-74_R1 (batch1)


title: ESC shRNA linc1629_1.1-110_R2 (batch1)


title: ESC shRNA NM_007624.1_R2 (batch1)


title: ESC shRNA linc1627_1.1-355_R2 (batch1)

value: shRNA knockdown of linc1627


title: ESC shRNA linc1627_1.1-355_R1 (batch1)


title: ESC shRNA linc1622_1.1-529_R2 (batch1)

value: shRNA knockdown of linc1622


title: ESC shRNA linc1623_1.1-235_R1 (batch1)


title: ESC shRNA linc1617_1.1-371_R2 (batch1)

value: shRNA knockdown of linc1617


title: ESC shRNA linc1616_1.1-325_R1 (batch1)

value: shRNA knockdown of linc1616


title: ESC shRNA linc1613_1.1-536_R1 (batch1)

value: shRNA knockdown of linc1613


title: ESC shRNA linc1612_1.1-469_R1 (batch1)

value: shRNA knockdown of linc1612


title: ESC shRNA linc1618_1.1-421_R1 (batch1)

value: shRNA knockdown of linc1618


title: ESC shRNA linc1622_1.1-529_R1 (batch1)


title: ESC shRNA linc1614_1.1-278_R1 (batch1)

value: shRNA knockdown of linc1614


title: ESC shRNA linc1607_1.1-210_R1 (batch1)

value: shRNA knockdown of linc1607


title: ESC shRNA linc1614_1.1-278_R2 (batch1)


title: ESC shRNA linc1603_1.1-167_R2 (batch1)

value: shRNA knockdown of linc1603


title: ESC shRNA linc1616_1.1-325_R2 (batch1)


title: ESC shRNA linc1615_1.1-82_R1 (batch1)

value: shRNA knockdown of linc1615


title: ESC shRNA linc1617_1.1-371_R1 (batch1)


title: ESC shRNA linc1604_1.1-350_R1 (batch1)

value: shRNA knockdown of linc1604


title: ESC shRNA linc1618_1.1-421_R2 (batch1)


title: ESC shRNA linc1603_1.1-167_R1 (batch1)


title: ESC shRNA linc1609_1.1-232_R1 (batch1)

value: shRNA knockdown of linc1609


title: ESC shRNA linc1611_1.1-450_R1 (batch1)

value: shRNA knockdown of linc1611


title: ESC shRNA linc1610_1.1-474_R2 (batch1)

value: shRNA knockdown of linc1610


title: ESC shRNA linc1613_1.1-536_R2 (batch1)


title: ESC shRNA linc1630_1.1-287_R1 (batch1)

value: shRNA knockdown of linc1630


title: ESC shRNA linc1602_1.1-107_R1 (batch1)

value: shRNA knockdown of linc1602


title: ESC shRNA linc1612_1.1-469_R2 (batch1)


title: ESC shRNA linc1607_1.1-210_R2 (batch1)


title: ESC shRNA linc1610_1.1-474_R1 (batch1)


title: ESC shRNA linc1602_1.1-107_R2 (batch1)


title: ESC shRNA linc1599_1.1-44_R1 (batch1)

value: shRNA knockdown of linc1599


title: ESC shRNA linc1601_1.1-337_R2 (batch1)

value: shRNA knockdown of linc1601


title: ESC shRNA linc1601_1.1-337_R1 (batch1)


title: ESC shRNA linc1598_1.1-50_R2 (batch1)

value: shRNA knockdown of linc1598


title: ESC shRNA linc1595_1.1-454_R2 (batch1)

value: shRNA knockdown of linc1595


title: ESC shRNA linc1563_1.1-3514_R1 (batch1)

value: shRNA knockdown of linc1563


title: ESC shRNA linc1572_1.1-63_R1 (batch1)

value: shRNA knockdown of linc1572


title: ESC shRNA linc1588_1.1-234_R2 (batch1)

value: shRNA knockdown of linc1588


title: ESC shRNA linc1562_2.1-1197_R2 (batch1)

value: shRNA knockdown of linc1562


title: ESC shRNA linc1582_1.1-258_R1 (batch1)

value: shRNA knockdown of linc1582


title: ESC shRNA linc1589_1.1-579_R1 (batch1)

value: shRNA knockdown of linc1589


title: ESC shRNA linc1598_1.1-50_R1 (batch1)


title: ESC shRNA linc1563_1.1-3514_R2 (batch1)


title: ESC shRNA linc1588_1.1-234_R1 (batch1)


title: ESC shRNA linc1581_1.1-1338_R2 (batch1)

value: shRNA knockdown of linc1581


title: ESC shRNA linc1595_1.1-454_R1 (batch1)


title: ESC shRNA NM_010066.2_R1 (batch1)

value: shRNA knockdown of NM_010066


title: ESC shRNA linc1562_2.1-1197_R1 (batch1)


title: ESC shRNA linc1581_1.1-1338_R1 (batch1)


title: ESC shRNA linc1543_1.1-802_R2 (batch1)

value: shRNA knockdown of linc1543


title: ESC shRNA linc1558_1.1-592_R1 (batch1)

value: shRNA knockdown of linc1558


title: ESC shRNA linc1537_1.1-1160_R1 (batch1)

value: shRNA knockdown of linc1537


title: ESC shRNA linc1582_1.1-258_R2 (batch1)


title: ESC shRNA linc1526_1.1-55_R1 (batch1)

value: shRNA knockdown of linc1526


title: ESC shRNA linc1557_1.1-842_R1 (batch1)

value: shRNA knockdown of linc1557


title: ESC shRNA linc1558_1.1-592_R2 (batch1)


title: ESC shRNA linc1604_1.1-350_R2 (batch1)

value: shRNA knockdown of linc1604


title: ESC shRNA linc1543_1.1-3855_R2 (batch1)


title: ESC shRNA linc1555_1.1-269_R2 (batch1)

value: shRNA knockdown of linc1555


title: ESC shRNA linc1552_2.1-838_R1 (batch1)

value: shRNA knockdown of linc1552


title: ESC shRNA linc1543_1.1-3855_R1 (batch1)


title: ESC shRNA linc1517_3.1-1638_R1 (batch1)

value: shRNA knockdown of linc1517


title: ESC shRNA linc1537_1.1-1160_R2 (batch1)


title: ESC shRNA linc1543_1.1-802_R1 (batch1)


title: ESC shRNA linc1540_1.1-6084_R1 (batch1)

value: shRNA knockdown of linc1540


title: ESC shRNA linc1526_1.1-55_R2 (batch1)


title: ESC shRNA linc1552_2.1-838_R2 (batch1)


title: ESC shRNA linc1557_1.1-842_R2 (batch1)


title: ESC shRNA linc1572_1.1-63_R2 (batch1)

value: shRNA knockdown of linc1572


title: ESC shRNA linc1517_3.1-1638_R2 (batch1)


title: ESC shRNA linc1559_1.1-1359_R1 (batch1)

value: shRNA knockdown of linc1559


title: ESC shRNA linc1555_1.1-269_R1 (batch1)


title: ESC shRNA linc1524_1.1-318_R1 (batch1)

value: shRNA knockdown of linc1524


title: ESC shRNA linc1524_1.1-318_R2 (batch1)


title: ESC shRNA linc1540_1.1-6084_R2 (batch1)


title: ESC shRNA linc1559_1.1-1359_R2 (batch1)


title: ESC shRNA linc1510_1.1-266_R4 (batch1)

value: shRNA knockdown of linc1510


title: ESC shRNA linc1510_1.1-266_R2 (batch1)


title: ESC shRNA linc1490_2.1-782_R2 (batch1)

value: shRNA knockdown of linc1490


title: ESC shRNA linc1490_2.1-612_R2 (batch1)


title: ESC shRNA linc1483_1.1-519_R1 (batch1)

value: shRNA knockdown of linc1483


title: ESC shRNA linc1473_1.1-220_R1 (batch1)

value: shRNA knockdown of linc1473


title: ESC shRNA linc1477_1.1-720_R1 (batch1)

value: shRNA knockdown of linc1477


title: ESC shRNA linc1470_1.1-402_R1 (batch1)

value: shRNA knockdown of linc1470


title: ESC shRNA linc1510_1.1-266_R3 (batch1)


title: ESC shRNA linc1470_1.1-402_R2 (batch1)


title: ESC shRNA linc1510_1.1-266_R1 (batch1)


title: ESC shRNA linc1473_1.1-220_R2 (batch1)


title: ESC shRNA linc1483_1.1-519_R2 (batch1)


title: ESC shRNA linc1490_2.1-782_R1 (batch1)


title: ESC shRNA linc1465_1.1-497_R2 (batch1)

value: shRNA knockdown of linc1465


title: ESC shRNA linc1477_1.1-720_R2 (batch1)


title: ESC shRNA linc1468_2.1-5203_R2 (batch1)

value: shRNA knockdown of linc1468


title: ESC shRNA linc1465_1.1-497_R1 (batch1)


title: ESC shRNA linc1468_2.1-5203_R1 (batch1)


title: ESC shRNA linc1471_1.1-60_R1 (batch1)

value: shRNA knockdown of linc1471


title: ESC shRNA linc1463_1.1-1421_R1 (batch1)

value: shRNA knockdown of linc1463


title: ESC shRNA linc1463_1.1-1421_R2 (batch1)


title: ESC shRNA linc1456_1.1-4387_R2 (batch1)

value: shRNA knockdown of linc1456


title: ESC shRNA linc1457_1.1-79_R1 (batch1)

value: shRNA knockdown of linc1457


title: ESC shRNA linc1454_1.1-681_R1 (batch1)

value: shRNA knockdown of linc1454


title: ESC shRNA linc1457_1.1-79_R2 (batch1)


title: ESC shRNA linc1450_1.1-604_R1 (batch1)

value: shRNA knockdown of linc1450


title: ESC shRNA linc1454_1.1-478_R1 (batch1)


title: ESC shRNA linc1454_1.1-681_R2 (batch1)


title: ESC shRNA linc1448_1.1-227_R2 (batch1)

value: shRNA knockdown of linc1448


title: ESC shRNA linc1435_1.1-242_R2 (batch1)

value: shRNA knockdown of linc1435


title: ESC shRNA linc1450_1.1-604_R2 (batch1)


title: ESC shRNA linc1456_1.1-4387_R1 (batch1)


title: ESC shRNA linc1434_1.1-3296_R2 (batch1)

value: shRNA knockdown of linc1434


title: ESC shRNA linc1434_1.1-3296_R1 (batch1)


title: ESC shRNA linc1419_1.1-1267_R2 (batch1)

value: shRNA knockdown of linc1419


title: ESC shRNA linc1425_1.1-298_R2 (batch1)

value: shRNA knockdown of linc1425


title: ESC shRNA linc1428_1.1-240_R1 (batch1)

value: shRNA knockdown of linc1428


title: ESC shRNA linc1435_1.1-977_R2 (batch1)


title: ESC shRNA linc1435_1.1-977_R1 (batch1)


title: ESC shRNA linc1435_1.1-242_R1 (batch1)


title: ESC shRNA linc1421_1.1-1095_R1 (batch1)

value: shRNA knockdown of linc1421


title: ESC shRNA linc1418_1.1-23_R1 (batch1)

value: shRNA knockdown of linc1418


title: ESC shRNA linc1421_1.1-1095_R2 (batch1)


title: ESC shRNA linc1419_1.1-1267_R1 (batch1)


title: ESC shRNA linc1412_3.1-611_R2 (batch1)

value: shRNA knockdown of linc1412


title: ESC shRNA linc1428_1.1-240_R2 (batch1)


title: ESC shRNA linc1412_3.1-611_R1 (batch1)


title: ESC shRNA linc1448_1.1-227_R1 (batch1)


title: ESC shRNA linc1413_1.1-333_R2 (batch1)

value: shRNA knockdown of linc1413


title: ESC shRNA linc1425_1.1-298_R1 (batch1)


title: ESC shRNA linc1413_1.1-333_R1 (batch1)


title: ESC shRNA linc1400_1.1-885_R2 (batch1)

value: shRNA knockdown of linc1400


title: ESC shRNA linc1412_1.1-223_R2 (batch1)


title: ESC shRNA linc1411_1.1-2359_R1 (batch1)

value: shRNA knockdown of linc1411


title: ESC shRNA linc1388_1.1-40_R2 (batch1)

value: shRNA knockdown of linc1388


title: ESC shRNA linc1400_1.1-885_R1 (batch1)


title: ESC shRNA linc1412_1.1-223_R1 (batch1)


title: ESC shRNA linc1391_1.1-53_R1 (batch1)

value: shRNA knockdown of linc1391


title: ESC shRNA linc1390_1.1-505_R2 (batch1)

value: shRNA knockdown of linc1390


title: ESC shRNA linc1390_1.1-505_R1 (batch1)


title: ESC shRNA linc1386_1.1-2478_R2 (batch1)

value: shRNA knockdown of linc1386


title: ESC shRNA linc1382_1.1-1060_R2 (batch1)

value: shRNA knockdown of linc1382


title: ESC shRNA linc1369_4.1-1077_R2 (batch1)

value: shRNA knockdown of linc1369


title: ESC shRNA linc1410_1.1-553_R1 (batch1)

value: shRNA knockdown of linc1410


title: ESC shRNA linc1389_2.1-1319_R2 (batch1)

value: shRNA knockdown of linc1389


title: ESC shRNA linc1454_1.1-478_R2 (batch1)

value: shRNA knockdown of linc1454


title: ESC shRNA linc1369_4.1-1077_R1 (batch1)


title: ESC shRNA linc1385_1.1-2506_R1 (batch1)

value: shRNA knockdown of linc1385


title: ESC shRNA linc1382_1.1-1060_R1 (batch1)


title: ESC shRNA linc1388_1.1-40_R1 (batch1)


title: ESC shRNA linc1389_2.1-1319_R1 (batch1)


title: ESC shRNA linc1386_1.1-2478_R1 (batch1)


title: ESC shRNA linc1490_2.1-612_R1 (batch1)

value: shRNA knockdown of linc1490


title: ESC shRNA linc1349_1.1-13_R4 (batch1)

value: shRNA knockdown of linc1349


title: ESC shRNA linc1349_1.1-13_R1 (batch1)


title: ESC shRNA linc1368_2.1-766_R2 (batch1)

value: shRNA knockdown of linc1368


title: ESC shRNA linc1368_2.1-766_R1 (batch1)


title: ESC shRNA linc1361_1.1-403_R2 (batch1)

value: shRNA knockdown of linc1361


title: ESC shRNA linc1366_1.1-1180_R2 (batch1)

value: shRNA knockdown of linc1366


title: ESC shRNA linc1366_1.1-1180_R1 (batch1)


title: ESC shRNA linc1361_1.1-403_R1 (batch1)


title: ESC shRNA linc1347_1.1-2917_R1 (batch1)

value: shRNA knockdown of linc1347


title: ESC shRNA linc1347_1.1-2917_R2 (batch1)


title: ESC shRNA linc1349_1.1-13_R2 (batch1)


title: ESC shRNA linc1328_1.1-510_R2 (batch1)

value: shRNA knockdown of linc1328


title: ESC shRNA linc1331_2.1-399_R1 (batch1)

value: shRNA knockdown of linc1331


title: ESC shRNA linc1316_2.1-1148_R1 (batch1)

value: shRNA knockdown of linc1316


title: ESC shRNA linc1316_2.1-1148_R2 (batch1)


title: ESC shRNA linc1313_1.1-1153_R1 (batch1)

value: shRNA knockdown of linc1313