title: invasive lung adenocarcinoma specimen AC0524

description: Gene expression data from human  mixed type invasive lung adenocarinoma

source_name: Microdissected invasive lung tumor

value: AdenoCarcinoma-mixed invasive

value: Ib


title: invasive lung adenocarcinoma specimen AC0422

status: Public on Sep 15 2011

type: RNA

city: New York

first: Charles

middle: A

last: Powell

state: NY

address: One Gustave Levy Place, Box 1232

department: MEDICINE/PULMONARY

country: USA

institute: Mount Sinai School of Medicine

hyb_protocol: cRNA was hybridized to the Affymetrix(Santa Clara,CA) Human Genome U133 Plus 2.0 Array

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

data_processing: Array data were normalized using the RMA algorithm with R/Bioconductor as implemented in BRB-Array Tools V4.1.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Biotinylated cRNA was generated by the modified Eberwine protocol

extract_protocol: Total RNA was extracted from laser capture microdissected cells using Rneasy minikit;Qiagen,Valencia,CA

tag: tissue

value: lung tumor

tag: pathological type

tag: gender

value: female

tag: age at dx

tag: stage grouping

value: IIIa

tag: t stage

tag: n stage


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U35

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: Lipodystrophic patient

hyb_protocol: The slides were scanned with GenePix 4200 AL (Axon Instruments, Molecular Devices, Silicon Valley, CA) at the resolution of 5 µm/pixel and at 16 bit depth.

scan_protocol: GPR files were imported in R v. 2.10 and preprocessed by the BioConductor package limma.

data_processing: quantile normalized log ratios (base2) from the median foregraound intensities with no background correction.

source_name: Dorsocervical adipose tissue

label_protocol: Labelled aRNAs was hybridized onto Whole Human Genome 4x44K microarrays (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s instructions. The slides were then washed according to the instructions with buffers from Agilent.

extract_protocol: The amplified RNA (aRNA, 5 µg/sample) was labelled using monoreactive Cy3 or Cy5 dyes (GE Healthcare, GE Life Sciences, Uppsala, Sweden) followed by purification according the manufacturer’s instructions.

treatment_protocol: Adipose tissue was homogenised using the Geneclean kit (Bio101 systems, Obiogene Inc., Carlsbad, CA). RNA was extracted with the RNeasy Lipid Tissue Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. Quantity and integrity of RNA were verified using RNA 6000 nanochips (Agilent 2100 Bioanalyser, Palo Alto, CA). Part of the isolated RNA was stored at -80°C until quantification of the target mRNAs by microarray.

value: Dorsocervical adipose tissue

tag: disease state

value: HIV+

tag: treatment result

value: developed lipodystrophy

source_name: Abdominal subcutaneous adipose tissue

value: Abdominal subcutaneous adipose tissue


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U27

description: Nonlipodystrophic patient

value: nonlipodystrophic


title: CHOP1224

type: genomic

city: Philadelphia

first: Jayanti

last: Jagannathan

state: PA

address: 34th & Civic center blvd

department: Oncology

institute: Childrens Hospital of Philadelphia

description: A key to the clinical annotation codes exists as a supplementary file linked to GSE19385.

hyb_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Tumor DNA

extract_protocol: DNA was extracted with Qiagen DNA extraction kit protocol

tag: stage

tag: risk

tag: mycn

tag: age

tag: shimada

tag: sex

tag: ploidy


title: C41-KH-N-2_ME

type: protein

city: Cambridge

first: Xinchen

last: Wang

state: MA

address: 32 Vassar St, D514

institute: MIT

hyb_protocol: 12.5 ul of the in vitro translation mix was added to 137.5 ul of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 uM zinc acetate/0.1% Tween 20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween 20 and once with PBS/0.01% Triton X 100.  After a one-hour incubation at room temperature, the array was washed once with PBS/0.5% Tween 20/50 uM zinc acetate and once with PBS/0.01% Triton X 100/50 uM zinc acetate.  Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 uM zinc acetate.  After a one-hour incubation at room temperature, the array was washed three times with PBS/0.05% Tween 20/50 uM zinc acetate and once with PBS/50 uM zinc acetate.

scan_protocol: Protein-bound microarrays were scanned using an Agilent microarray scanner at 2 uM resolution to detect Cy5-conjugated antibody.

data_processing:
Microarray TIF images were analyzed using ImaGene version 7.5 software (BioDiscovery)
We provide several scores for each 8-mer or 9-mer sequence in each experiment: (1) Median Intensity. (2) Z-Score – transformed kmer median intensity. (3) E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots.
Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

molecule: protein

source_name: FOXP1-ES forkhead domain purified from C41 cells - replicate 2

label_protocol: T7-GST tagged proteins were not labelled after purification

extract_protocol: The forkhead domains were cloned as BamHI-BamHI fragments into pGEX-2T. C41 and XL1 cells were transformed with the plasmids and the expression of the GST fusion proteins was induced by IPTG at 37C for 4h. The proteins were purified using Glutathione Sepharose 4B resine according the manufacturer's instructions. The GST-fusion protein concentrations and purification qualitty were estimated by SDS-PAGE using serial dilutions.

tag: isoform

tag: domain

value: forkhead domain

tag: isoform purified from

value: C41 cells


title: C41-KH-A-2_ME

source_name: FOXP1 forkhead domain purified from C41 cells - replicate 2


title: noninvasive lung adenocarcinoma specimen AC0418

description: Gene expression data from human noninvasive lung adenocarinoma tumor (BAC)

source_name: Microdissected noninvasive lung tumor

tag: tissue

tag: pathological type

value: BronchioloAlveolar Carcinoma

tag: gender

value: Ia


title: noninvasive lung adenocarcinoma specimen AC0516

tag: age at dx

tag: stage grouping

tag: t stage


title: CHOP1165

scan_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols


title: C41-KH-N-1_ME

source_name: FOXP1-ES forkhead domain purified from C41 cells - replicate 1


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U26

description: Nonlipodystrophic patient

tag: disease state

tag: treatment result


title: C41-KH-A-1_ME

source_name: FOXP1 forkhead domain purified from C41 cells - replicate 1


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U24

description: Nonlipodystrophic patient


title: CHOP2551

data_processing: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols

tag: stage

tag: risk


title: noninvasive lung adenocarcinoma specimen AC9908

tag: n stage


title: CHOP2548

label_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols

tag: mycn

tag: age

tag: shimada


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U25

description: Nonlipodystrophic patient


title: invasive lung adenocarcinoma specimen AC0436


title: Gsk-3a-/- ESCs Rep1

city: Columbus

first: Christopher

last: Phiel

state: OH

address: 700 Children's Drive W432

institute: The Research Institute at Nationwide Children's Hospital

hyb_protocol: Following fragmentation, labeled cRNA was hybridized to the Mouse 430 2.0 array. Hybridization was allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: CEL files were generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals were generated using the Background Adjustment Using Sequence Information (gcrma 2.14.1) Package in R version 2.8.0. Data was used to determine differential gene expression by pair-wise comparisons and statistical analysis was performed using both the Linear Models for Microarray Data (limma 2.16.5) and Multiple testing using SAM and Efron's empirical Bayes approaches (siggenes 1.16.0) packages. The genes that were altered two-fold either way with significance at either a 10% FDR or adjusted P value of <= 0.05 were sorted and used for further interpretation of the microarray data.

organism: Mus musculus

source_name: Total RNA from Gsk-3a-/- ESCs

label_protocol: The Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) was used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA was synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA was achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA was purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content was measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.

growth_protocol: Feeder-free wild-type, GSK-3a-/-, Gsk-3b-/-, and Gsk-3 DKO ESCs were grown on gelatin coated plates in high glucose DMEM (GIBCO) supplemented with 15% fetal bovine serum (Hyclone), 1X non-essential amino acids, 1X sodium pyruvate, 2mM L-glutamine, 1X penicillin/streptomycin (GIBCO), 55 mM 2-mercaptoethanol, and 1000 units/ml ESGRO (Millilpore). Media was replenished every other day.

extract_protocol: Cells were collected by addition of 0.25% trypsin EDTA to PBS washed cells and incubated for 1 minute at 37C. Trypsin was inactivated by addition of twice the volume of ESC media. Cells were washed in PBS, and resuspended in TRIzol (Invitrogen), and RNA was isolated following the manufacturer's protocol. RNA was then further purified with the RNeasy RNA cleanup procedure (Qiagen).

tag: genotype/variation

tag: cell type

value: embryonic stem cells


title: CHOP1211

tag: sex

tag: ploidy


title: XL1-KH-N_ME

source_name: FOXP1-ES forkhead domain purified from XL1 cells

tag: isoform

tag: domain

tag: isoform purified from

value: XL1 cells


title: invasive lung adenocarcinoma specimen AC0521

tag: tissue

tag: pathological type

tag: gender

tag: age at dx

tag: stage grouping


title: CHOP1226

tag: stage

tag: risk


title: CHOP1139

tag: mycn


title: CHOP1149

tag: age


title: Snf2-null

city: University Park

first: Sujana

last: Ghosh

address: 453 North Frear

department: BMMB

institute: The Pennsylvania State University

description:
polyA RNA
The Δsnf2 strain was analyzed by genome-wide expression profiling with DNA microarrays.

del_Snf2_top_t-red.gpr
del_Snf2_bottom_t-green.gpr

hyb_protocol: Two µg of mRNA was used for hybridizations. Slides were placed in a hybridization chamber at 42C for ~12-16 hrs. Arrays were then washed in 2x SSC (+0.1 % SDS), 1x SSC, 0.2x SSC and 0.05x SSC, each for 1 min, prior to drying followed by treatment with DyeSaver (Genisphere) to preserve signal intensity.

scan_protocol: Microarrays were scanned and quantitated with a GenePix 4000A scanner and GenePix 4.0 software (Axon Instruments).

data_processing: Microarray image files were processed as follows:  1) Spots where greater than 25% of the pixels were saturated were eliminated; 2) The mean foreground signal minus mean background signal had to be greater than the sum of the mean background signal plus one standard deviation of the background intensity; 3) Ratios of “test”/“reference” were log2 transformed. “Test” samples were ∆SnAC and ∆snf2, BY4741 against an independent BY4741 reference, and SNF2-2FLAG test against an independent SNF2-2FLAG reference;  4) From this ratio, the corresponding ratio of the spiking controls (median) was subtracted; and 5)  Dye-swapped replicates were averaged.

organism: Saccharomyces cerevisiae

source_name: Snf2-null mutant

label_protocol: The cDNA generated by reverse transcription using aminoallyl-dUTP was labeled with fluorescent dyes (Cy3 and Cy5).

growth_protocol: All of the yeast strains were grown in YPD at 25C to an O.D of 0.8.

extract_protocol: Total RNA was isolated using the hot-phenol method followed by poly (A+) mRNA purification using Oligo-dT Cellulose (Ambion). Externally generated Bacillus subtilis polyadenylated transcripts (Phe, Lys, Dap, Thr, Trp) were added to the total RNA based on A600 optical density of the culture.  These serve as spiking controls.

treatment_protocol: Cells were rapidly harvested by centrifugation at room temperature, washed with RNase-free DEPC (diethyl pyrocarbonate)-treated double-distilled water, and then frozen in liquid nitrogen in less than 15 minutes to minimize exposure to changes that might affect expression.

tag: background strain

tag: genotype

source_name: Wild type

value: wild type


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U23

description: Nonlipodystrophic patient

tag: disease state

tag: treatment result


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U20

description: Lipodystrophic patient


title: CHOP1124

tag: shimada

tag: sex

tag: ploidy


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U19

description: Nonlipodystrophic patient


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U22

description: Nonlipodystrophic patient


title: noninvasive lung adenocarcinoma specimen AC0413

value: male

tag: t stage

tag: n stage


title: CHOP1111


title: XL1-KH-A_ME

source_name: FOXP1 forkhead domain purified from XL1 cells

tag: isoform

tag: domain

tag: isoform purified from


title: invasive lung adenocarcinoma specimen AC0420

tag: tissue

tag: pathological type

value: AdenoCarcinoma-mixed invasive

tag: gender

tag: age at dx

tag: stage grouping

value: Ib


title: SnAc domain deletion

description:
polyA RNA
The ∆SnAC strain was analyzed by genome-wide expression profiling with DNA microarrays.

SnAc_top_t-red.gpr
SnAc_bottom_t-green.gpr

source_name: SnAc domain deletion mutant

tag: background strain

value: SnAc domain deletion

value: wild type, Snf2-2FLAG


title: Snf2-2FLAG (WT)

description:
polyA RNA
Wild type strain (Snf2-2FLAG, PSY2) was analyzed by genome-wide expression profiling with DNA microarrays.

Snf2-2FLAG_top_t-red.gpr
Snf2-2FLAG_bottom_t-green.gpr

tag: genotype


title: BY4741 (WT)

description:
polyA RNA
Wild type strain (BY4741) was analyzed by genome-wide expression profiling with DNA microarrays.

BY4741_top_t-red.gpr
BY4741_bottom_t-green.gpr


title: invasive lung adenocarcinoma specimen AC0450

value: lung tumor


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U16

description: Lipodystrophic patient

value: Dorsocervical adipose tissue

tag: disease state

value: HIV+


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U18

description: Lipodystrophic patient

tag: treatment result

value: developed lipodystrophy

value: Abdominal subcutaneous adipose tissue


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U17

description: Lipodystrophic patient


title: invasive lung adenocarcinoma specimen AC0546

value: female


title: H5_rat_mammary gland

city: Burlington

first: Yogi

last: Misra

state: Vermont

address: 570 Main street

department: Animal Science

institute: UVM

description: Gene expression data from Rat inguinal mammary gland during the metestrus phase of the reproductive cycle

hyb_protocol: Fragmentation and Biotin labeling was performed using  4ug of cDNA using the NuGEN Encore reagents and h ybridized to the Rat 230 2.0 GeneChip for 16 hr at 45C at 60 rpm, double stained with streptavidin-PE using the Affymetrix 450 fluidics station and scanned with the Affymetrix  3000-G7 scanner

scan_protocol: The gene chips were scanned with Affymetrix  3000-G7 scanner

data_processing: Raw oligonucleotide array data image is summarized by one probe intensity using Affymetrix GCOS software. Probe statistics are background corrected, normalized, and summarized using the R (R Development Core Team, 2009)/Bioconductor (Gentleman et al., 2004) aroma affymetrix  package (Bengtsson et al., 2008), which implements the Robust Multichip Average (RMA) statistic of Speed and coworkers (Bolstad et al., 2003; Irizarry et al., 2003). Affymetix MAS5 presence/absence calls were made using the Bioconductor affy package (Gautier et al., 2004) and provided as a Series Supplementary files [analysis_results.txt]

organism: Rattus norvegicus

source_name: hormone treatment group

label_protocol: Biotinylated cDNA were prepared using the reagents of  NuGEN Ovation V2 from 80 ng of  total RNA

growth_protocol: Fifteen, 3 month old post-pubertal virgin Lewis rats were kept in the University of Vermont small animal care facility. Rats were housed in the air and temperature-controlled cage shelves on a 12-hour light/dark cycle and were fed rat chow (RMH 3000, Lab Diet, Scott Distributing, Inc. MA) and water ad libitum

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

treatment_protocol: Rats were randomly assigned to three groups (5 rats per group): control (C), pregnancy (P) and hormone treatment (H). The P group animals had a full-term pregnancy (21-23 days) and rats in the group H were implanted subcutaneously on the dorsal midline with two silastic capsules [(0.078 inch inner diameter, 0.125 inch outer diameter) x 2 cm long; Dow Corning, Midland, MI) filled separately with 100 μg ethynyl estradiol (Sigma, St. Louis, MO) packed in a cellulose matrix (Sigma) and 30 mg of megesterol acetate (Sigma) for 21 days. The control animals had neither the hormone treatment nor being pregnant. The animals in C and P groups were also implanted with sham capsules filled with cellulose matrix only.

tag: strain

value: Lewis rats

value: Female

tag: age

value: 3 month old

tag: physiological stage

value: Met-estrus

tag: tissue type

value: Mammary gland Inguinal left


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U14

description: Nonlipodystrophic patient

value: nonlipodystrophic


title: invasive lung adenocarcinoma specimen AC0545

value: Ia

tag: t stage

tag: n stage


title: invasive lung adenocarcinoma specimen AC0647

value: AdenoCarcinoma-mixed invasive

value: IIIa


title: H4_rat_mammary gland


title: CHOP1050

tag: stage

tag: risk

tag: mycn

tag: shimada

tag: sex

tag: ploidy


title: H3_rat_mammary gland

tag: gender


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U13

description: Lipodystrophic patient

tag: tissue


title: noninvasive lung adenocarcinoma specimen AC0411

tag: pathological type

value: BronchioloAlveolar Carcinoma

tag: age at dx

tag: stage grouping


title: noninvasive lung adenocarcinoma specimen AC0544

value: IIb


title: CHOP0977


title: H2_rat_mammary gland

tag: strain


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U12

description: Lipodystrophic patient

tag: disease state

tag: treatment result


title: H1_rat_mammary gland

tag: age

tag: physiological stage

tag: tissue type


title: CHOP0979

tag: stage


title: CHOP1030

tag: risk


title: CHOP0544

tag: mycn


title: noninvasive lung adenocarcinoma specimen AC0642

value: lung tumor

tag: t stage

tag: n stage


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U11

description: Nonlipodystrophic patient

value: Dorsocervical adipose tissue


title: P9_rat_mammary gland

source_name: pregnancy group


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U7

description: Lipodystrophic patient

value: HIV+


title: invasive lung adenocarcinoma specimen AC0541

source_name: Microdissected invasive lung tumor

value: Ib


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U8

description: Lipodystrophic patient

source_name: Dorsocervical adipose tissue

value: developed lipodystrophy

value: Abdominal subcutaneous adipose tissue


title: noninvasive lung adenocarcinoma specimen AC0540

value: female


title: P7_rat_mammary gland

source_name: pregancy group

value: Lewis rats

value: Female


title: invasive lung adenocarcinoma specimen AC0543


title: CHOP0839

source_name: Tumor DNA

tag: shimada

tag: sex

tag: ploidy


title: CHOP0525


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U6

description: Lipodystrophic patient

tag: tissue

source_name: Abdominal subcutaneous adipose tissue


title: noninvasive lung adenocarcinoma specimen AC0538

tag: pathological type

tag: gender

tag: age at dx


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U4

description: Nonlipodystrophic patient

tag: disease state


title: P3_rat_mammary gland

tag: strain

value: 3 month old

value: Met-estrus


title: P1_rat_mammary gland

tag: age

value: Mammary gland Inguinal left


title: P2_rat_mammary gland

tag: physiological stage


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U5

description: Nonlipodystrophic patient

tag: treatment result

value: nonlipodystrophic


title: CHOP0543

tag: stage


title: invasive lung adenocarcinoma specimen AC0435

value: AdenoCarcinoma-mixed invasive

value: male

tag: stage grouping

value: Ia


title: invasive lung adenocarcinoma specimen AC0437


title: invasive lung adenocarcinoma specimen AC0334


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U2

description: Lipodystrophic patient


title: CHOP0811

tag: risk

tag: mycn


title: CHOP1061


title: CHOP0807


title: CHOP0753


title: CHOP0767


title: C4_rat_mammary gland

source_name: control group

tag: tissue type


title: CHOP0773

tag: shimada


title: noninvasive lung adenocarcinoma specimen AC0031

source_name: Microdissected noninvasive lung tumor

value: BronchioloAlveolar Carcinoma

tag: t stage

tag: n stage


title: Dorsocervical vs. abdominal subcutaenous adipose tissue U1

description: Lipodystrophic patient

tag: tissue


title: C6_rat_mammary gland


title: A3B4L3

city: Sippy Downs

first: Nicole

last: Ertl

state: Queensland

address: 90 Sippy Downs Drive

department: FOSHE - GeneCology

country: Australia

institute: University of the Sunshine Coast

hyb_protocol: Agilent protocol (quick-amp low input)

scan_protocol: Axon Scanner, 520 gain

data_processing:
Normalisation was carried out using the GeneSpring GX 11.0 program with a threshold raw signal of 1.0, a percentile shift algorithm to 75th percentile, and no base line transformation. Unpaired t-tests with Benjamini and Hochberg FDR (Benjamini & Hochberg 1995) multiple testing corrections were used for the statistical analysis of the data to correct for the occurrence of type 1 errors, with the significance value (p) for all statistical tests set at 0.05.

GeneSpring data was not saved, and has not been submitted to GEO. The normalisation can be repeated using the  foreground-background intensity data with the normalisation steps described above.

organism: Penaeus merguiensis

source_name: Cuticle light

label_protocol: Agilent protocol (quick-amp low input)

extract_protocol: Trizol protocol, Invitrogen

value: cuticle excised from light prawn


title: invasive lung adenocarcinoma specimen AC0529

value: lung tumor

tag: pathological type


title: noninvasive lung adenocarcinoma specimen AC0028

tag: gender

value: IIb


title: C2_rat_mammary gland


title: invasive lung adenocarcinoma specimen AC0423

tag: age at dx

value: IIa


title: C5_rat_mammary gland


title: CHOP0742

tag: sex

tag: ploidy


title: C1_rat_mammary gland

tag: strain

tag: age


title: CHOP0736


title: A3B2A4

scan_protocol: Axon Scanner, 610 gain

source_name: Cuticle albino

value: cuticle excised from albino prawn


title: CHOP0748


title: A3B1A3

scan_protocol: Axon Scanner, 590 gain


title: CHOP0750


title: invasive lung adenocarcinoma specimen AC0414

value: IIIa


title: invasive lung adenocarcinoma specimen AC0419


title: invasive lung adenocarcinoma specimen AC0415

value: Ib


title: A2B3L2

scan_protocol: Axon Scanner, 500 gain


title: invasive lung adenocarcinoma specimen AC0517

value: female


title: CHOP0719


title: CHOP0718


title: noninvasive lung adenocarcinoma specimen AC0012


title: CHOP0730


title: CHOP0633


title: invasive lung adenocarcinoma specimen AC0410


title: A2B1L4

scan_protocol: Axon Scanner, 540 gain


title: CHOP0714


title: A3B3D3

scan_protocol: Axon Scanner, 530 gain

source_name: Cuticle dark

value: cuticle excised from dark prawn


title: noninvasive lung adenocarcinoma specimen AC9909


title: 3_RL_48h_LY317615+

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data of LY317615-treated RL cell line replicate 3.

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hr 30 minutes at 45°C on GeneChip® Gene 1.0 ST array according to the standard Affymetrix protocol. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The Gene 1.0 ST arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA).

data_processing: A preliminary data quality evaluation and RMA normalization were performed with the Expression Console Software GCOS version 1.4 (Affymetrix Inc., Santa Clara, CA, USA).

source_name: B cell lymphoma RL cell line, treated

label_protocol: 5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual).

growth_protocol: The RL cell line carrying the t(14;18) (from DSMZ) was cultured at 37 °C in a 5% CO2-humidified atmosphere in RPMI-1640 (Euroclone Ltd, UK) supplemented with 10% fetal bovine serum (FBS; Euroclone Ltd, UK), 2 mM L-glutamine, and 100 U/ml each penicillin and streptomycin (Euroclone Ltd).

extract_protocol: Total RNA was isolated using TRIzol (Life Technologies, Inc., Rockville, MD, USA), and then purified using the RNeasy Total RNA Isolation Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: RL cells were treated with 2.5 mM LY317615 for 48h.

tag: cell line

value: RL

tag: cell type

value: B cell lymphoma

tag: treatment

tag: treatment time

value: 48 hours

tag: replicate


title: A1B4D4


title: 2_RL_48h_LY317615+

description: Gene expression profiling data of LY317615-treated RL cell line replicate 2.


title: A2B2D2

scan_protocol: Axon Scanner, 560 gain


title: 1_RL_48h_LY317615+

description: Gene expression profiling data of LY317615-treated RL cell line replicate 1.


title: invasive lung adenocarcinoma specimen AC0207

tag: stage grouping


title: A1B2L1


title: A2B4A2


title: CHOP0605

tag: stage

tag: risk

tag: mycn

tag: shimada


title: noninvasive lung adenocarcinoma specimen AC0106

tag: tissue

tag: pathological type

tag: t stage

tag: n stage


title: noninvasive lung adenocarcinoma specimen AC0305

tag: gender

tag: age at dx


title: 3_RL_48h_LY317615-

description: Gene expression profiling data of untreated RL cell line replicate 3.

source_name: B cell lymphoma RL cell line, untreated

value: untreated


title: A1B1D1

scan_protocol: Axon Scanner, 550 gain


title: 2_RL_48h_LY317615-

description: Gene expression profiling data of untreated RL cell line replicate 2.


title: CHOP0610

tag: age

tag: sex

tag: ploidy


title: intracellular Streptococcus pyogenes

city: Stockholm

first: Erika

last: Hertzén

address: Karolinska University Hospital, Huddinge, Center for Infectious Medicine, F59

country: Sweden

institute: Karolinska Institutet

description: 3 replicates

hyb_protocol: Hybridization buffer was prepared and consisted of: LNA dt Blocker, Nuclease free water, 2x hybridization buffer. Finally it was mixed together with cDNA tagged with Alexa 546 or Alexa 647. The tubes were incubated at 80 degrees C for 10 min and then left at 65 degrees until loading of the arrays. Meanwhile, the arrays were warmed up to 65 degrees C in an oven. Then the hybridization mix was applied and the array were sealed with a glass coverslip. Also 2X SSC was added to each end of the cassette to prevent drying out the sample and the casettes were sealed with clips and put in a 55 degrees C oven for 3 hours (dark). Then the arrays were removed from the cassette and put in room temp 0.2% SDS 2X SSC for 3 min, then they were transferred to 42 degrees C 0.2% SDS 2X SSC and incubated in 42 degrees C oven for 15 min, then room temp 2X SSC for 15 min and finally room temp 0.2X SSC for 15 min. (All incubations in dark).The slides were then centrifuged to remove all residual liquid and placed dark in a closed container and analysed within 30 min.

scan_protocol: Scanning was done by a GenePix 4000B (Axon Instruments, Inc.) using the GenePixPro 5.1 software.

data_processing: All transcriptional and statistical analyses were undertaken in silico using GeneSpring GX 11 (Agilent Technologies). Background-subtracted data were filtered and raw fluoresecene values below 50 were discareded as fold-changes at this level may lead to misinterpretation. Data were normalized to the median and presented in log scale for analysis based on fold-change.

label: Alexa 546

organism: Streptococcus pyogenes

source_name: Intracellular

label_protocol: cDNA was labeled with Alexa Fluor 546/647 by using a 3DNA Array 900 MPX kit (Genisphere), 2ug cDNA/sample was tailed, and tagged according to the protocol provided by Genisphere. Nuclease-free water was added to the cDNA and heated to 95 C for 10 min afterwhich it was transferred to ice for 2 min. Tailing buffer, dTTO and Terminal Deoxynucleotidyl Transferase was added and incubated for 30 min at 37 degrees C. Ligation to 3DNA Capture Sequence was done by heating the tailed DNA to 95 degrees C for 10 min and immeldiately transferred to ice for 10 min. Then appropriate  Ligation mix (either Alexa 546 or Alexa 647) and T4 DNA ligase was added and incubated at room temperature (21 degrees) for 30 min. 0.5M EDTA was added to stop the reaction and TE buffer was added. Then the tagged DNA was purified using the Qiagen MinElute PCR Purification Kit.

extract_protocol: RNA was extracted using RiboPure Bacteria kit (Ambion) and purified RNA was reversely transcribed into complementary DNA using SuperScript III reverse transcriptase (Invitrogen) all methods as described in the included manuals.

treatment_protocol: Bacteria were either grown in cellculture media (RPMI 1640) for the extracellular control or added to human monocyte derived macrophages in RPMI 1640. Infected macrophages were at the time of extraction detached with a rubber police man, pooled and centriguged and then treated with RLT buffer.

tag: infection

value: intracellular Streptococcus pyogenes


title: CHOP0618


title: invasive lung adenocarcinoma specimen AC0304

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

value: AdenoCarcinoma-mixed invasive

value: male


title: Osthole treated Replicate 1

status: Public on Sep 14 2011

city: Changchun

first: Lu

last: Yu

address: Xi'an Road 5333

country: China

institute: Jilin university

description: Biological replicate 1 of 2. Control DMSO treated, harvested after several passages.

hyb_protocol: The samples were hybridized with Agilent whole genome oligo microarray,performed by Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242)in Agilent’s SureHyb Hybridization Chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned with the Agilent DNA microarray scanner (part number G2505B) using settings recommended by Agilent Technologies. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: The resulting text files extracted from Agilent Feature Extraction Software (version 10.5.1.1) were imported into the Agilent GeneSpring GX software (version 11.0) for further analysis. The microarray data sets were normalized in the Agilent GeneSpring GX software. After filtered by the Agilent GeneSpring GX software, 4841 rows were obtained.

organism: Mycobacterium tuberculosis

source_name: M. tuberculosis_Osthole

label_protocol: The samples were labeled using the Agilent Quick Amp labeling kit.

growth_protocol: Mycobacterium tuberculosis H37Rv was incubated in a rotary shaker. Subsequently, Osthole stock solution, prepared in dimethyl sulfoxide (DMSO), and DMSO was added to the culture,respectively. Then, the the cells were further incubated for a certain time.

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

tag: strain

source_name: M. tuberculosis_DMSO


title: Osthole treated Replicate 2


title: 1_RL_48h_LY317615-

description: Gene expression profiling data of untreated RL cell line replicate 1.

tag: cell line

tag: cell type

tag: treatment

tag: replicate


title: noninvasive lung adenocarcinoma specimen AC0403

value: BronchioloAlveolar Carcinoma

tag: stage grouping

value: Ia


title: CHOP0667

tag: stage

tag: risk

tag: mycn

tag: shimada


title: CHOP0594


title: S3: corneas dissected 3 days after sham operated (lens left in) at stage 50

city: Dunedin

first: Caroline

last: Beck

address: 340 Great King Street

department: Zoology

country: New Zealand

institute: University of Otago

scan_protocol: 7G Plus GeneChip Scanner 3000

data_processing: RMA normalised using GenePattern software

organism: Xenopus laevis

label_protocol: Nugen WT-Ovation pico kit

growth_protocol: tadpoles were cultured at 20 degrees in 0.1 x MMR salts overnight and then in 25 degrees in water until harvested at day 3 after surgery

extract_protocol: RNA later, Ambion RNAqueous micro kit used to extract RNA and treat with DNAse I as protocol.

tag: developmental stage

value: stage 50, Nieuwkoop and Faber

tag: genotype

value: wildtype

tag: tissue

value: cornea


title: R3: corneas dissected 3 days after removal of lens at stage 50


title: A1B3A1

value: cuticle excised from albino prawn


title: S4: corneas dissected 3 days after sham operated (lens left in) at stage 50


title: CHOP0583

scan_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols

tag: age


title: extracellular Streptococcus pyogenes

description: 2 replicates

label: Alexa 647

source_name: Extracellular

value: extracellular Streptococcus pyogenes


title: L1: whole lens excised stage 50

source_name: whole lens excised stage 50

value: whole lens


title: R1: corneas dissected 3 days after removal of lens at stage 50


title: L2: whole lens excised stage 50


title: L3: whole lens excised stage 50


title: R2: corneas dissected 3 days after removal of lens at stage 50


title: CHOP0593

tag: sex


title: S1: corneas dissected 3 days after sham operated (lens left in) at stage 50


title: Small_inestine-SpecificPathogenFree-JTX_treated-rep3

city: Shinjuku

first: Masahiro

last: Yamamoto

state: Tokyo

address: 35 Shinano-machi

department: Department of Kampo Medicine

country: Japan

institute: Keio University School of Medicine

description:
SPF-SI-6-3
Gene expression data from small intestines of specific pathogen free mice

hyb_protocol: The labeled cRNA was fragmented, hybridized to MG-U74Av2 array (Affymetrix, Santa Clara, CA) using an Affymetrix fluidics station according to the Affymetrix protocols.

scan_protocol: GeneChips were scanned with an Affymetrix scanner, according to the Affymetrix protocols.

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

label_protocol: The labeled cRNA was prepared from by in vitro transcription (Enzo Biochem, New York, NY).

growth_protocol: GF mice were housed in a Trexler-type flexible film isolator in a standard germ free state and screened on a weekly basis for germ-free status by sampling feces sterilely and culturing on MRS-agar plates under aerobic and anaerobic conditions. All the GF, SPF, ex-GF mice were kept in a 12: 12-h light/dark cycle and at a temperature of 22±2°C.

extract_protocol: Total RNA was extracted from mice (n = 3 per each group) using TRIzol (Life Technologies, Rockville, TX) and re-purified by RNeasy spin columns (Quiagen, Valencia, CA), according to the manufacturer’s instructions.

treatment_protocol: Nine week old mice (n=3) were sacrificed by cervical dislocation and the small intestine was dissected (SI was not divided into proximal and distal sections and was treated as a single intestinal section). Tissue destined for RNA extraction were flash-flozen in liquid nitrogen after washing with ice-cold PBS.

value: IQI

tag: gender

value: small intestine

tag: enteric flora status

value: specific pathogen free (SPF)


title: Small_inestine-SpecificPathogenFree-urtreated-rep2

description:
SPF-SI-2-3
Gene expression data from small intestines of specific pathogen free mice

tag: strain


title: Small_inestine-GermFree-JTX_treated-rep3

description:
GF-SI-10-3
Gene expression data from small intestines of germ-free mice

value: germ-free (GF)


title: Small_inestine-SpecificPathogenFree-urtreated-rep3

description:
SPF-SI-5-3
Gene expression data from small intestines of specific pathogen free mice


title: POS3

first: Yupu

last: Liang

address: 1230 York Avenue

institute: The Rockefeller University

description: Replicate 3 of 3.

hyb_protocol: Standard Illumina hybridization protocol (58 degrees for 16-20 hours).

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was normalized using the LumiExpresso() function (lumi Bioconductor package). Probes with non-zero detectable probe ratio of each probe in all  samples were selected (using the lumi function detectionCall() ). Total number of probes considered for further analysis is 20,178.

label: Biotin

source_name: Afp::GFP transgenic XEN stem cell line, BMP4 treated, Afp::GFP-positive

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

growth_protocol: Afp:GFP transgenic XEN cells were grown in N2B27 media.

extract_protocol: RNA was extracted using the Qiagen RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Thermo Scientific nanodrop 1000.

treatment_protocol: BMP4 was added to XEN cell media. GFP-positive vs. GFP-negative cells were flow sorted.

value: AFP::GFP transgenic extraembryonic endoderm (XEN) stem cells

value: BMP4 growth factor

tag: cell subpopulation

value: GFP+


title: CHOP0457

description: A key to the clinical annotation codes exists as a supplementary file linked to GSE19385.

tag: ploidy


title: POS1

description: Replicate 1 of 3.

tag: cell type

tag: treatment


title: Small_inestine-SpecificPathogenFree-JTX_treated-rep1

description:
SPF-SI-3-3
Gene expression data from small intestines of specific pathogen free mice


title: NEG1

description: Replicate 1 of 3.

source_name: Afp::GFP transgenic XEN stem cell line, BMP4 treated, Afp::GFP-negative

value: GFP-


title: CHOP0398


title: NEG3

description: Replicate 3 of 3.


title: Small_inestine-GermFree-JTX_treated-rep1

description:
GF-SI-8-3
Gene expression data from small intestines of germ-free mice

value: male


title: Small_inestine-GermFree-urtreated-rep3

description:
GF-SI-7-3
Gene expression data from small intestines of germ-free mice


title: Small_inestine-GermFree-JTX_treated-rep2

description:
GF-SI-9-3
Gene expression data from small intestines of germ-free mice


title: CHOP0574


title: Small_inestine-GermFree-urtreated-rep2

description:
GF-SI-6-3
Gene expression data from small intestines of germ-free mice


title: mA5_B3

description: Replicate 3 of 3.

source_name: Afp::GFP transgenic XEN stem cell line, BMP4 treated


title: mA5_B2

description: Replicate 2 of 3.


title: Small_inestine-SpecificPathogenFree-urtreated-rep1

description:
SPF-SI-1-3
Gene expression data from small intestines of specific pathogen free mice


title: NEG2

description: Replicate 2 of 3.


title: POS2

description: Replicate 2 of 3.


title: mA5_B1

description: Replicate 1 of 3.


title: CHOP0348

source_name: Tumor DNA


title: CHOP0255


title: CHOP0200


title: CHOP0186


title: mA5_C3

description: Replicate 3 of 3.

source_name: Afp::GFP transgenic XEN stem cell line, untreated


title: mA5_C2

description: Replicate 2 of 3.


title: Colon-BALB/c-JTX_treated-rep3

description:
BALB-LI-5-3
Gene expression data from colon of specific pathogen free BALB/c mice

treatment_protocol: Nine week old mice (n=3) were sacrificed by cervical dislocation and the colon was dissected (the colon was not divided into proximal and distal sections and was treated as a single intestinal section). Tissue destined for RNA extraction were flash-flozen in liquid nitrogen after washing with ice-cold PBS.

value: BALB/c

value: Colon


title: Small_inestine-SpecificPathogenFree-JTX_treated-rep2

description:
SPF-SI-4-3
Gene expression data from small intestines of specific pathogen free mice


title: Colon-BALB/c-nontreated-rep3

description:
BALB-LI-1-3
Gene expression data from colon of specific pathogen free BALB/c mice

source_name: Colon-BALB/c-nontreated


title: Colon-BALB/c-JTX_treated-rep1

description:
BALB-LI-5-1
Gene expression data from colon of specific pathogen free BALB/c mice


title: Colon-BALB/c-nontreated-rep2

description:
BALB-LI-1-2
Gene expression data from colon of specific pathogen free BALB/c mice


title: Colon-SpecificPathogenFree-JTX_treated-rep3

description:
SPF-LI-8-4
Gene expression data from colon of specific pathogen free mice


title: Colon-BALB/c-nontreated-rep1

description:
BALB-LI-1-1
Gene expression data from colon of specific pathogen free BALB/c mice


title: Colon-SpecificPathogenFree-JTX_treated-rep1

description:
SPF-LI-3-4
Gene expression data from colon of specific pathogen free mice


title: Colon-GermFree-JTX_treated-rep3

description:
GF-LI-10-4
Gene expression data from colon of germfree mice


title: Colon-SpecificPathogenFree-JTX_treated-rep2

description:
SPF-LI-4-4
Gene expression data from colon of specific pathogen free mice


title: mA5_C1

description: Replicate 1 of 3.


title: explant VEGFR2i

city: jerusalem

first: Yuval

last: Dor

address: ein-karem

country: Israel

institute: Hadassah medical school

description: pancreatic buds explanted and treated with VEGFR2i (n=5, pooled)

hyb_protocol: For washing staining and scanning we used standard fluidic protocol FS450_0007 GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays

data_processing: The arrays were RMA normalized using Partek Genomic Suite 6.5. Differentially regulated genes were selected based on p-values and ratios using ttest.

label_protocol: target preparation was performed according to the standard Affymetrix user manual GeneChip® Whole Transcript (WT) Sense Target Labeling Assay chapter 4 from 300ng total RNA

growth_protocol: RNA was isolated from pancreatic buds of Pdx1-tTA (n=3) and littermate Pdx1-tTA; TET-VEGF (n=3) e12.5 embryos, or from e12.5 wild type pancreatic buds explanted and treated  with VEGFR2i (n=5) or vehicle (n=5) for 2 day

extract_protocol: For transcriptome analysis, RNA was isolated using QIAGEN RNeasy micro Kit

tag: genotype/variation

value: wild type

value: pancreatic bud


title: explant vehicle

description: pancreatic buds explanted and treated with vehicle (n=5, pooled)

scan_protocol: For washing staining and scanning we used standard fluidic protocol FS450_0007 GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays

treatment_protocol: RNA was isolated from pancreatic buds of Pdx1-tTA (n=3) and littermate Pdx1-tTA; TET-VEGF (n=3) e12.5 embryos, or from e12.5 wild type pancreatic buds explanted and treated  with VEGFR2i (n=5) or vehicle (n=5) for 2 day


title: Pdx1-tTA; TET-VEGF TR

description: pancreatic buds of Pdx1-tTA; TET-VEGF e12.5 embryos (n=3, pooled) technical repeat

source_name: pancreatic buds of Pdx1-tTA; TET-VEGF e12.5 embryos technical repeat

value: Pdx1-tTA; TET-VEGF


title: CHOP0047

description: A key to the clinical annotation codes exists as a supplementary file linked to GSE19385.

tag: stage


title: Pdx1-tTA TR

description: pancreatic buds of Pdx1-tTA littermate e12.5 embryos (n=3, pooled) technical repeat

source_name: pancreatic buds of Pdx1-tTA littermate e12.5 embryos technical repeat


title: Pdx1-tTA

description: pancreatic buds of Pdx1-tTA littermate e12.5 embryos (n=3, pooled)


title: explant VEGFR2i TR

description: pancreatic buds explanted and treated with VEGFR2i (n=5, pooled) technical repeat

source_name: pancreatic buds explanted and treated with VEGFR2i technical repeat


title: Colon-GermFree-JTX_treated-rep1

description:
GF-LI-8-4
Gene expression data from colon of germfree mice


title: CHOP0283

tag: risk


title: CHOP0171

tag: mycn


title: Colon-GermFree-JTX_treated-rep2

description:
GF-LI-9-4
Gene expression data from colon of germfree mice


title: H1299 at T12, biological rep1

city: Seoul

first: Woong Yang

last: Park

address: 28 Yongondong, Chongnogu

department: Biochemistry and Molecular Biology

country: South Korea

institute: Seoul National University

description: miRNA expression data from H1299 12hr after  ionizing irradiation (2 Gy)

hyb_protocol: The labeled samples were washed and hybridized in duplicate to mirVana miRNA Bioarrays (Ambion) using the mirVana miRNA Bioarray Essentials Kit.

scan_protocol: mirVana protocol

data_processing: The levels of miRNA hybridization were determined using GenePix Pro 6.0 software as recommended by the manufacturer.  The background-adjusted intensity for each miRNA was subjected to a global variance stabilization normalization (VSN) procedure

source_name: H1299 12hr after ionizing irradiation

label_protocol: Purified miRNAs were labeled using the mirVana miRNA Array Labeling Kit and coupled to the Cy5 Post-Labeling Reactive Dye (Amersham, GE Healthcare Bio-Sciences, Piscataway, NJ, USA).

growth_protocol: The lung cancer cell line H1299  was maintained as a monolayer in RPMI 1640 medium supplemented with 10 % fetal bovine serum, 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine at 37°C in humidified 5% CO2 .

extract_protocol: microRNA was extracted using the mirVana miRNA isolation kit (Ambion, Austin, TX, USA) according to the manufacturer’s protocols.

treatment_protocol: The exponentially growing cells were irradiated with 2 Gy of γ-radiation using a 4 MV linear accelerator (Clinac 4/100, Varian, Palo Alto, CA). No irradiated cells were used as a negative control. The irradiated and control cells were incubated for various periods of times (0, 2, 4, 8, 12 and 24 hours) before isolating total RNA.

tag: cell line

value: lung cancer cells


title: H1299 at T8, biological rep1

description: miRNA expression data from H1299 8hr after  ionizing irradiation (2 Gy)

source_name: H1299 8hr after ionizing irradiation


title: H1299 at T8, biological rep2


title: 46_B-0_1-24

city: Oslo

first: Erta

last: kalanxhi

address: Montebello 0310

country: Norway

institute: Oslo University Hospital

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: performed with Illumina BeadStudio 3.1.3.0 Gene Expression Module 3.4.0

label: biotin, Cy3

source_name: bystander fibroblast 26 h

label_protocol: Performed with Illumina® TotalPrep RNA Amplification Kit

growth_protocol: The cells were grown in DMEM supplied with 1% L-Glutamine and Penicillin/ Streptomycin and 20% FBS and kept at 37°C and 5% CO2.

extract_protocol: Total RNA from four, or three independent experiments was isolated from cells irradiated with 0.1 Gy and bystander fibroblasts 4, 8 and 26 h after irradiation (or 2, 6, and 24 h after medium transfer from irradiated to bystander cells) using Pure Link RNA mini kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Irradiated cells were irradiated with 0.1 Gy alpha-particle radiation. Control cells were incubated in medium from unirraidated cells 2 h after irradiation. Bystander cells were incubated with medium from cells irradiated with 0.1 Gy alpha-particle radiation, 2 h after irradiation. Extraction of RNA was done 4, 6 and 8 h after irradiation.

value: immortalized hTERT

value: fibroblasts

tag: treatment group

value: bystander fibroblast 26 h


title: H1299 at T24, biological rep2

description: miRNA expression data from H1299 24hr after  ionizing irradiation (2 Gy)

source_name: H1299 24hr after ionizing irradiation


title: 47_B-0_1-24

description: replicate 3


title: 44_B-0-24

description: replicate 4

source_name: bystander ctrl fibroblast 26 h

value: bystander ctrl fibroblast 26 h


title: 45_B-0_1-24

description: replicate 1


title: H1299 at T12, biological rep2


title: H1299 at T4, biological rep2

description: miRNA expression data from H1299 4hr after  ionizing irradiation (2 Gy)

source_name: H1299 4hr after ionizing irradiation


title: H1299 at T4, biological rep1


title: 48_B-0_1-24

description: replicate 4


title: H1299 at T2, biological rep1

description: miRNA expression data from H1299 2hr after  ionizing irradiation (2 Gy)

source_name: H1299 2hr after ionizing irradiation


title: H1299 at T0, biological rep2

description: miRNA expression data from H1299 before ionizing irradiation

source_name: H1299 non-small lung carcinoma cell line before ionizing irradiation


title: H1299 at T2, biological rep2


title: H1299 at T0, biological rep1


title: H1299 at T24, biological rep1


title: BY4742, biological replicate 3

city: Baltimore

first: Jessica

last: Dymond

state: MD

address: 733 N. Broadway BRB 320

department: High Throughput Biology Center

institute: Johns Hopkins University School of Medicine

description: Gene expression data from wild type strain

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

scan_protocol: Flourescence was detected using the Affymetrix G3000 GeneArray Scanner

data_processing: Data were analyzed using Partek Genomics Suite 6.5 (update 6.11.0321). Briefly, the data were generated by importing all interrogating probes without filtration,  normalized with RMA, and converted to log2 notation.

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: Yeast was inoculated in rich medium (YPD) at 0.1 OD/ml and grown at 30C to 0.4 OD/ml.

extract_protocol: Total RNA was extracted with hot phenol, then further purified using an RNeasy column (Qiagen).

value: whole cell

tag: genotype

value: log-phase growth


title: Pdx1-tTA; TET-VEGF

description: pancreatic buds of Pdx1-tTA; TET-VEGF e12.5 embryos (n=3, pooled)

tag: tissue

tag: developmental stage


title: BY4742, biological replicate 2

tag: age


title: 43_B-0-24

description: replicate 3


title: 42_B-0-24

description: replicate 2


title: 41_B-0-24

description: replicate 1


title: 38_B-0_1-6

description: replicate 2

source_name: bystander fibroblast 8 h

value: bystander fibroblast 8 h


title: 37_B-0_1-6

description: replicate 1


title: 40_B-0_1-6

description: replicate 4


title: 39_B-0_1-6

description: replicate 3


title: BY4742, biological replicate 1


title: BY4741, biological replicate 1


title: SynIXR-22D, biological replicate 3

description: Gene expression data from synIXR haploid

value: synIXR


title: BY4741, biological replicate 2


title: SynIXR-22D, biological replicate 2


title: BY4741, biological replicate 3


title: explant vehicle TR

description: pancreatic buds explanted and treated with vehicle (n=5, pooled) technical repeat

source_name: pancreatic buds explanted and treated with vehicle technical repeat


title: SynIXR-6B, biological replicate 3


title: SynIXR-6B, biological replicate 2


title: 36_B-0-6

description: replicate 3

source_name: bystander ctrl fibroblast 8 h

value: bystander ctrl fibroblast 8 h


title: SynIXR-22D, biological replicate 1


title: SynIXR-1D, biological replicate 2


title: Normal 9

city: Toronto

first: Saswati

last: Sen

state: ON

address: 555 university avenue

country: Canada

institute: Hospital for Sick Children

description:
Gene expression data from bone marrow mononuclear cells.
Fresh bone marrow samples were obtained from nine patients with SDS.  Bone marrow samples were collected into syringes containing preservative-free heparin.  The bone marrow mononuclear cell fraction was separated using Ficoll-Hypaque density gradient centrifugation.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized according to the manufacturers instructions on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip4 Scanner 3000 (Affymetrix Inc.)

data_processing: Gene expression signal, detection call, signal log ratio and change call were calculated using GeneChip Operating Software by the statistical algorithm published previously by Affymetrix (Hubbell et al, 2002; Liu et al, 2002)

source_name: Bone marrow mononuclear cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: Bone marrow mononuclear cells

value: SBDS Positive

tag: age (y)

tag: disease state

value: Shwachman-Diamond syndrome (SDS)


title: 34_B-0-6

description: replicate 1


title: SynIXR-6B, biological replicate 1


title: Normal 6


title: SynIXR-1D, biological replicate 3


title: Normal 7


title: 35_B-0-6

description: replicate 2


title: Normal 5


title: 30_B-0_1-2

description: replicate 2

source_name: bystander fibroblast 4 h

value: bystander fibroblast 4 h


title: 31_B-0_1-2

description: replicate 3


title: 29_B-0_1-2

description: replicate 1


title: 27_B-0-2

description: replicate 3

source_name: bystander ctrl fibroblast 4 h

value: bystander ctrl fibroblast 4 h


title: Small_inestine-GermFree-urtreated-rep1

description:
GF-SI-5-3
Gene expression data from small intestines of germ-free mice

tag: strain

value: IQI

tag: gender

value: male

value: small intestine

tag: enteric flora status

value: germ-free (GF)


title: SDS 9

tag: cell type

value: SBDS mutant


title: SynIXR-1D, biological replicate 1


title: 25_B-0-2

description: replicate 1

value: immortalized hTERT

value: fibroblasts


title: 24_IRR-0_1-24

description: replicate 3

source_name: irradiated (0.1 Gy) fibroblast 26 h

value: irradiated (0.1 Gy) fibroblast 26 h


title: Colon-BALB/c-JTX_treated-rep2

description:
BALB-LI-5-2
Gene expression data from colon of specific pathogen free BALB/c mice

value: BALB/c

value: Colon

value: specific pathogen free (SPF)


title: Male vs. Asexual female at long day, biological replicate 2

city: Coral Gables

first: Rebecca

last: Duncan

state: FL

address: 1301 Memorial Dr.

department: Department of Biology

institute: University of Miami

hyb_protocol: Four competitive hybridizations were made for each biological repliate.  For aphid line W109, the hybridizations were made as follows: male -> asexual female (long day) -> sexual female -> asexual female (short day) -> male where the direction of the arrow indicates Cy3 -> Cy5 labeling.  For aphid line W115, hybridization was performed with the reverses labeling.

scan_protocol: Microarrays were scanned using a GenePix 4000B scanner (Molecular Devices).  The resulting images were analyzed using GenePix Pro 6.1 (Molecular Devices) and subject to quality control using Acuity 4.0 (Molecular Devices).

data_processing: Raw data were processed using Linear Models for Microarray Data (LIMMA) implemented in R.  Loess normalization was used, followed by normalization between arrays using a quantile algorithm implemented in LIMMA. Differential expression and false discovery rates were assessed using a linear model and empirical Bayes moderated F statistics.

organism: Myzus persicae

source_name: Whole male aphids, line W115

label_protocol: 1 µg total RNA was labeled using an Amino Allyl MessageAmp aRNA Amplification Kit (Ambion) and Cy3- and Cy5-NGS ethers (Amersham).

extract_protocol: Total RNA was extracted from ten flash frozen aphids per aphid line per treatment using an RNeasy Mini Kit (Qiagen).

treatment_protocol: Asexual females at long day were grown from an isofemale clone at 20ºC under a 14h/10h light/dark cycle. Sexual morphs were induced by changing the growth conditions to 16ºC under a 10h/14h light/dark cycle.  Males, sexual females, and asexual females at short day were all collected when sexual morphs were present in the culture.

tag: aphid line

tag: Sex

value: Male

tag: reproductive morph

value: Sexual

source_name: Whole asexual female aphids at long day, line W115

value: Female

value: Asexual (long day)


title: 26_B-0-2

description: replicate 2


title: Sexual female vs. Asexual female at short day, biological replicate 2

source_name: Whole sexual female aphids, line W115

source_name: Whole asexual female aphids at short day, line W115

value: Asexual (short day)


title: Asexual female at long day vs. Sexual female, biological replicate 2


title: 28_B-0-2

description: replicate 4

value: bystander ctrl fibroblast 4 h


title: SDS 7

value: Bone marrow mononuclear cells

value: Shwachman-Diamond syndrome (SDS)


title: 23_IRR-0_1-24

description: replicate 2


title: SDS 4


title: Adult bone marrow NCSC, replicate 2

city: Liège

first: sabine

last: wislet

address: 1 avenue de l'hopital

department: GIGA-Neurosciences

country: Belgium

institute: university of Liège

description:
NCSC2
Mice background is C57BL/6 x SV129 as described in Glejzer et al. 2011 (PMID 20976520).

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChip Scanner 3000 7G, AGCC v1.1.

data_processing: Normalization and data filtering were performed using BRB-ArrayTools software version 3.8.1 developed by Dr. Richard Simons and the BRB-ArrayTools Development Team, http://linus.nci.nih.gov./BRB-ArrayTools.html. We used the GCRMA algorithm as the normalization step. The statistical analysis was done with the Class Comparison tool. The statistical analysis was done with BRB ArrayTools software.

source_name: bone marrow stromal cells isolated from double-transgenic mice wnt1/cre-R26R-lacZ, NCSC

label_protocol: 3' IVT Express kit (Affymetrix).

growth_protocol: Cells were grown in Mesencult (Stem Cells Technology) medium for a minimum of 5 passages before clonal selection.

extract_protocol: RNeasy mini kit (Qiagen).

treatment_protocol: None.

tag: background

value: 10 weeks

value: adult

value: female

value: bone marrow

value: neural crest stem cell (NCSC)


title: SDS 8

value: SBDS mutant


title: Normal 1

value: SBDS Positive

value: unknown


title: 22_IRR-0_1-24

description: replicate 1

value: immortalized hTERT

value: fibroblasts

value: irradiated (0.1 Gy) fibroblast 26 h


title: Adult bone marrow NCSC, replicate 3

description:
NCSC3
Mice background is C57BL/6 x SV129 as described in Glejzer et al. 2011 (PMID 20976520).


title: Adult bone marrow MSC, replicate 2

description:
MSC2
Mice background is C57BL/6 x SV129 as described in Glejzer et al. 2011 (PMID 20976520).

source_name: bone marrow stromal cells isolated from double-transgenic mice wnt1/cre-R26R-lacZ, MSC

value: mesenchymal stem cell (MSC)


title: 18_IRR-0-24

description: replicate 2

source_name: irradiated ctrl (0 Gy) fibroblast 26 h

value: irradiated ctrl (0 Gy) fibroblast 26 h


title: SDS 3


title: Adult bone marrow MSC, replicate 3

description:
MSC3
Mice background is C57BL/6 x SV129 as described in Glejzer et al. 2011 (PMID 20976520).


title: SDS 5


title: SDS 6


title: 17_IRR-0-24

description: replicate 1


title: Adult bone marrow NCSC, replicate 1

description:
NCSC1
Mice background is C57BL/6 x SV129 as described in Glejzer et al. 2011 (PMID 20976520).


title: 20_IRR-0-24

description: replicate 3


title: 16_IRR-0_1-6

description: replicate 4

source_name: irradiated (0.1 Gy) fibroblast 8 h

value: irradiated (0.1 Gy) fibroblast 8 h


title: SDS 2


title: Asexual female at short day vs. Male, biological replicate 2

value: Female

value: Asexual (short day)

value: Male

value: Sexual


title: Adult bone marrow MSC, replicate 1

description:
MSC1
Mice background is C57BL/6 x SV129 as described in Glejzer et al. 2011 (PMID 20976520).

value: 10 weeks

value: adult


title: 15_IRR-0_1-6

description: replicate 3


title: NO36

city: New York

description: Hybridized to 250K_Nsp

hyb_protocol: Labeled cDNA were hybridized, according to the Afymetrix protocol, for 16-18 hr, at 60 rpm, at 50C on a GeneChip Genome-Wide Human SNP Array 500K. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G Scanner.

data_processing: The data were analyzed with GTYPE using Affymetrix default analysis settings and the BRLMM algorithm.

source_name: Mesothelioma cell line

label_protocol: 500ng of DNA starting material was digested, ligated with adaptors, PCR amplified, cleaned-up, fragmented, and labeled according to the Affymetrix protocol.

growth_protocol: All cells were grown in RPMI with 10% FCS, penicillin/streptomycin at 37 degrees C and 5% CO2.

extract_protocol: Genomic DNA was extracted using the Qiagen Dneasy Blood & Tissue Kit according to the manufacturerss instructions.

treatment_protocol: No treatment.

value: mesothelioma cells


title: SDS 1

value: Bone marrow mononuclear cells

value: Shwachman-Diamond syndrome (SDS)


title: Asexual female at long day vs. Male, biological replicate 1

source_name: Whole asexual female aphids at long day, line W109

value: Asexual (long day)

source_name: Whole male aphids, line W109


title: Asexual female at short day vs. Sexual female, biological replicate 1

source_name: Whole asexual female aphids at short day, line W109

source_name: Whole sexual female aphids, line W109


title: Male vs. Asexual female at short day, biological replicate 1


title: Sexual female vs. Asexual female at long day, biological replicate 1


title: Embryonic day 15.5 diabetes replicate 3

city: Singapore

first: Srinivasan

last: Dinesh Kumar

address: 50 Nanyang Drive, Research Techno Plaza

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

description: Gene expression data from heart tissue isolated from embryonic day 15.5 diabetes exposed mouse

hyb_protocol: The labeled cRNA was then cleaned up, fragmented, and hybridized to Mouse Genome 430 2.0 Array (Affymetrix, CA, USA).

scan_protocol: Arrays were using an Affymetrix 3000 7G scanner.

data_processing: CEL files were exported to Affymetrix Expression Console Version 1.1 and RMA normalization (using EC1.1) was carried out.

source_name: Heart tissue

label_protocol: The RNA samples were processed according to the Affymetrix 3’ IVT Express protocol and Origen Lab’s SOP for 3’ IVT Express analysis. Briefly, 100 ng of total RNA was reverse transcribed to produce cDNA, which was subsequently used as a template to create biotin- labeled aRNA (amplified RNA).

extract_protocol: Total RNA from developing hearts was extracted using RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Diabetes mellitus was induced in 8 week-old female mice by an intraperitoneal injection of streptozotocin (STZ, 75mg/kg body weight, Sigma, USA) dissolved in citrate buffer (0.01 M, pH 4.5) for three successive days. Blood glucose level was examined one week after STZ injection using Glucometer Elite (Bayer, USA). Mice with non-fasting blood glucose level exceeding 16 mmol/l were used as experimental diabetic mice. In contrast, control mice maintained the normal blood glucose levels (4– 6 mmol/l) before and during pregnancy. Timed mating was carried out by placing four female mice with one normal male mouse in a cage overnight. The day when a copulation plug was observed was counted as embryonic day 0.5 (E0.5).  Time-mated pregnant mice were divided into two groups control and diabetes.  At E13.5 and E15.5, pregnant mice were anaesthetized with pentobarbital (150 mg/kg body wt, intraperitoneally) and embryos were collected after Caesarean. For each experiment, hearts were isolated from embryos from the two groups at different time points. The developmental stage, E13.5 corresponds to ~6 weeks of human gestation, hence it was chosen for this study.  At this stage all 4 chambers of the heart were clearly distinguishable, and the outflow tract was evident. In addition, the heart phenotype was apparent in embryos from diabetic mice. The embryos with cardiac malformations from diabetic mice were classified as diabetic group and normal embryos from diabetic and non-diabetic mice were used as control groups.

value: Swiss Albino

tag: disease status

value: diabetes


title: DEX siFoxA1 rep 2_v4

city: Helsinki

first: Olli

middle: A.

last: Jänne

department: Inst. of Biomedicine/Physiology

institute: University of Helsinki

description: 5417622013_H, HumanHT-12_V4

scan_protocol: Standard Illumina scan protocol

data_processing: The data were normalised using quantile normalisation with BeadStudio Program from Illumina.

source_name: DEX siFoxA1

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

growth_protocol: LNCaP-1F5 cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS), 2 mM L-glutamine, and 10 mM HEPES supplemented with antibiotics (penicillin and streptomycin).

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kitwith DNaseI treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: FoxA1 depletion was done using siRNA smartpool specific to FoxA1 mRNA. Both parental and FoxA1 depleted cells were grown in charcoal stripped medium for 3 days followed by treated with 100 nM 5a-dihydrotestosterone (DHT) or 100 nM DEX for 24 hours followed by RNA isolation.

tag: cell line

tag: genotype/variation

value: FoxA1 depleted


title: Embryonic day 15.5 control replicate 3

description: Gene expression data from heart tissue isolated from embryonic day 15.5 control mouse

value: control


title: Embryonic day 13.5 diabetes replicate 3

description: Gene expression data from heart tissue isolated from embryonic day 13.5 diabetes exposed mouse


title: 9_IRR-0-6

description: replicate 1

source_name: irradiated ctrl (0 Gy) fibroblast 8 h

value: immortalized hTERT

value: fibroblasts

tag: treatment group

value: irradiated ctrl (0 Gy) fibroblast 8 h


title: Embryonic day 15.5 control replicate 1


title: Embryonic day 15.5 diabetes replicate 2


title: Embryonic day 15.5 diabetes replicate 1


title: DHT siFoxA1 rep1_v3

description: 5050496020_G, HumanHT-12_V3

source_name: DHT siFoxA1


title: DHT siFoxA1 rep 2_v3

description: 5050496020_H, HumanHT-12_V3


title: Vehicle siFoxA1 rep2_v3

description: 5050496020_F, HumanHT-12_V3

source_name: Vehicle siFoxA1


title: DHT parental rep1_v3

description: 5050496020_C, HumanHT-12_V3

source_name: DHT parental

value: parental


title: 11_IRR-0-6

description: replicate 3


title: Embryonic day 15.5 control replicate 2


title: 14_IRR-0_1-6

description: replicate 2

value: irradiated (0.1 Gy) fibroblast 8 h


title: 10_IRR-0-6

description: replicate 2


title: 13_IRR-0_1-6

description: replicate 1


title: Embryonic day 13.5 diabetes replicate 2


title: DEX siFoxA1 rep1_v4

description: 5417622013_G, HumanHT-12_V4


title: Vehicle siFoxA1 rep1_v3

description: 5050496020_E, HumanHT-12_V3


title: Vehicle parental rep2_v3

description: 5050496020_B, HumanHT-12_V3

source_name: Vehicle parental


title: Vehicle siFoxA1 rep2_v4

description: 5417622013_F, HumanHT-12_V4


title: Vehicle siFoxA1 rep1_v4

description: 5417622013_E, HumanHT-12_V4


title: DHT parental rep 2_v3

description: 5050496020_D, HumanHT-12_V3


title: 8_IRR-0_1-2

description: replicate 3

source_name: irradiated (0.1 Gy) fibroblast 4 h

value: irradiated (0.1 Gy) fibroblast 4 h


title: 12_IRR-0-6

description: replicate 4


title: 7_IRR-0_1-2

description: replicate 2


title: DEX parental rep1_v4

description: 5417622013_C, HumanHT-12_V4

source_name: DEX parental


title: Vehicle parental rep1_v3

description: 5050496020_A, HumanHT-12_V3


title: DEX parental rep 2_v4

description: 5417622013_D, HumanHT-12_V4


title: Vehicle parental rep1_v4

description: 5417622013_A, HumanHT-12_V4


title: 5_IRR-0_1-2

description: replicate 1


title: Embryonic day 13.5 diabetes replicate 1


title: Vehicle parental rep2_v4

description: 5417622013_B, HumanHT-12_V4


title: Pol2t_2

status: Public on Sep 13 2011

city: Rehovot

first: Ariel

last: Gispan

address: P.O. Box 26

department: Molecular Genetics

institute: Weizmann Institute of Science

hyb_protocol: Agilent yeast ChIP-on-chip180Kx4 arrays

scan_protocol: Agilent microarray scanner Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Matlab was used to read the files, background subtraction and LOWESS normalization.

label_protocol: DNA was digested with DpnII and amplified by four rounds of random-octamer-primed Exo-Klenow DNA synthesis (Invitrogen BioPrime ArrayCGH amplification kit) with amino-allyl modified nucleotides. DNA was labeled with Cy dyes

growth_protocol: Strains were grown 12-16 hr at 30˚C in YPD. The strains were diluted to O.D 0.05 in YPD +10 μg/ml doxycycline and harvested after 6-7 hr at logaritmic phase .

extract_protocol: DNA from FACS-sorted cells was extracted using the MasterPure Yeast DNA purification kit

treatment_protocol: 10 μg/ml doxycycline

tag: cell cycle phase

value: S phase

value: G2 phase


title: Embryonic day 13.5 control replicate 3

description: Gene expression data from heart tissue isolated from embryonic day 13.5 control mouse


title: Embryonic day 13.5 control replicate 2


title: 2-Gb5ko

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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

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

data_processing: RMA by software Partek

growth_protocol: All animal studies were approved by the NIDDK/NIH Animal Care and Use Committee.

treatment_protocol: Mice were maintained in a pathogen-free facility, with 4–5 animals  per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food  and water ad libitum. Age and sex matched littermate cohorts were used for all the  experiments to account for potential strain differences.

tag: tissue

value: non-cerebellar portion of brain


title: 3_IRR-0-2

description: replicate 2

source_name: irradiated ctrl (0 Gy) fibroblast 4 h

value: irradiated ctrl (0 Gy) fibroblast 4 h


title: Pol2t_1


title: 4_IRR-0-2

description: replicate 3


title: Sld5t_2


title: Dpb11t_1


title: 5-Gb5wt

value: wild type


title: 1-Gb5ko


title: 6-Gb5wt


title: 4-Gb5wt


title: Pol30t_1


title: Sld5t_1


title: Cdc45t_2


title: 3-Gb5ko


title: Dpb11t_2


title: Pol12t_1


title: Embryonic day 13.5 control replicate 1

tag: age


title: Cdc45t_1


title: Pol12t_2


title: 1_IRR-0-2

description: replicate 1


title: 1-WT

source_name: WT

treatment_protocol: Mice were maintained in a pathogen-free facility, with 4–5 animals per cage in a temperature-controlled room with a 12-h light/dark cycle and access to food and water ad libitum. Age and sex matched littermate cohorts were used for all the experiments to account for potential strain differences.

value: Brain Tissues


title: 4-KO

source_name: Gb5 KO


title: 2-WT


title: 6-KO


title: 3-WT


title: MIY_day_7-4

city: Boston

first: Amit

last: Sinha

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Loss of Dot1l in MLL-AF9 murine leukemia.

hyb_protocol: 5 μg of labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.

scan_protocol: GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.

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

source_name: Dot1l flox/flox day 7 after transduction with control

label_protocol: Amplified cDNA was labeled using the Nugene Encore TM Biotin Module.

growth_protocol: Leukemias were generated by injecting 100 000 MLL-AF9-GFP transduced Dot1l flox/flox 4 days after transduction into B6129 recipients. Bulk leukemia cells were isolated from leukemic mice.

extract_protocol: Total RNA was extracted using Trizol. RNA was prepared using the Nugen Ovation Pico WTA system.

treatment_protocol: Sorted GFP-positive Dot1l flox/flox MLL-AF9 leukemia cells were transduced with retroviral Cre-YFP or YFP control vector. GFP/YFP positive cells were sorted on days 3, 5, and 7.

value: MLL-AF9 leukemia cells

tag: genotype

value: Dot1l flox/flox

tag: days after transduction


title: Triple-negative breast cancer_419

city: Frankfurt

first: Thomas

last: Karn

address: Theodor-Stern-Kai 7

country: Germany

description:
TNBC_419
Gene expression data from primary breast tumors.

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45°C on the GeneChip HG-U133A array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

source_name: primary breast cancer tissue

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kits according to the manufacturer's instructions.

extract_protocol: Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Samples were snap frozen and stored at -80°C.

value: triple-negative breast cancer

tag: lymph node status (0

value: negative, 1:positive):1

tag: grade (12

tag: tumor size (1

tag: event-free interval (months)

tag: event (1

tag: cohort

tag: biopsy type (1

value: surgical, 2:core needle):1

tag: chemotherapy treatment (yes/no)

value: NO

tag: neoadjuvant chemotherapy (yes/no)


title: Triple-negative breast cancer_267

description:
TNBC_267
Gene expression data from primary breast tumors.

value: surgical, 2:core needle):2

value: YES


title: MIY_day_7-3

tag: strain

tag: cell type


title: MIY_day_5-2

source_name: Dot1l flox/flox day 5 after transduction with control


title: MIY_day_5-5


title: Triple-negative breast cancer_269

description:
TNBC_269
Gene expression data from primary breast tumors.

value: negative, 1:positive):0


title: Triple-negative breast cancer_266

description:
TNBC_266
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_268

description:
TNBC_268
Gene expression data from primary breast tumors.


title: 5-KO

tag: genotype/variation


title: Triple-negative breast cancer_270

description:
TNBC_270
Gene expression data from primary breast tumors.


title: MIY_day_5-3


title: Cre_day_5-5

source_name: Dot1l -/- day 5 after transduction with cre

value: Dot1l -/-


title: Cre_day_7-1

source_name: Dot1l -/- day 7 after transduction with cre


title: MIY_day_5-1


title: MIY_day_7-2


title: Triple-negative breast cancer_264

description:
TNBC_264
Gene expression data from primary breast tumors.


title: Cre_day_5-4


title: Triple-negative breast cancer_418

description:
TNBC_418
Gene expression data from primary breast tumors.


title: MIY_day_7-1


title: Cre_day_7-3


title: Triple-negative breast cancer_265

description:
TNBC_265
Gene expression data from primary breast tumors.


title: MIY_day_5-4


title: Triple-negative breast cancer_271

description:
TNBC_271
Gene expression data from primary breast tumors.


title: Cre_day_7-2


title: Triple-negative breast cancer_262

description:
TNBC_262
Gene expression data from primary breast tumors.


title: Cre_day_5-3


title: Triple-negative breast cancer_258

description:
TNBC_258
Gene expression data from primary breast tumors.


title: MIY_day_3-4

source_name: Dot1l flox/flox day 3 after transduction with control


title: MIY_day_3-1


title: Triple-negative breast cancer_259

description:
TNBC_259
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_256

description:
TNBC_256
Gene expression data from primary breast tumors.


title: MIY_day_3-3


title: Triple-negative breast cancer_260

description:
TNBC_260
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_263

description:
TNBC_263
Gene expression data from primary breast tumors.


title: Cre_day_5-2

description: Loss of Dot1l in MLL-AF9 murine leukemia.


title: MIY_day_3-2


title: Triple-negative breast cancer_072

description:
TNBC_072
Gene expression data from primary breast tumors.

value: HH


title: Triple-negative breast cancer_254

description:
TNBC_254
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_071

description:
TNBC_071
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_070

description:
TNBC_070
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_257

description:
TNBC_257
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_255

description:
TNBC_255
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_068

description:
TNBC_068
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_067

description:
TNBC_067
Gene expression data from primary breast tumors.


title: Cre_day_3-4

source_name: Dot1l -/- day 3 after transduction with cre


title: Cre_day_5-1


title: Triple-negative breast cancer_253

description:
TNBC_253
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_261

description:
TNBC_261
Gene expression data from primary breast tumors.


title: Cre_day_3-1


title: Cre_day_3-3


title: Cre_day_3-5


title: Triple-negative breast cancer_073

description:
TNBC_073
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_066

description:
TNBC_066
Gene expression data from primary breast tumors.


title: Cre_day_3-2


title: Triple-negative breast cancer_065

description:
TNBC_065
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_063

description:
TNBC_063
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_062

description:
TNBC_062
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_069

description:
TNBC_069
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_061

description:
TNBC_061
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_059

description:
TNBC_059
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_028

description:
TNBC_028
Gene expression data from primary breast tumors.

value: FRA


title: Triple-negative breast cancer_060

description:
TNBC_060
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_027

description:
TNBC_027
Gene expression data from primary breast tumors.


title: epiWAT HGI replicate 10

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent In Situ Hybridization Kit Plus. Samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and hybridized at 65C for 17 hours at 4rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations using a Cy5-dyesaver as published (Anal Biochem 2007_363_315).

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (v 9.5.1.1) to obtain raw median signal and background values for both Cy5 and Cy3. Spots with a mean signal higher than twice the background value over all arrays were considered to be expressed. Data was normalized according to Pellis et al., (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, LOWESS normalization, and log2 transformation.

source_name: epididymal white adipose tissue, high fat, high glycemic index diet (HGI)

label_protocol: 500 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol version 3.1 , as described previously (Am J Clin Nutr 2008; 87:181-189).

extract_protocol: Total RNA was isolated from epididymal WAT as described (Faseb J 2009; 23:1092-1101), quantified using Nanodrop and qualified using Experion Automated Electrophoresis System.

treatment_protocol: Animals were fed a purified high fat (30 energy% fat) diet, as published (Faseb J 2009; 23:1092-1101). The carbohydrate fraction of the high fat diets had either a low glycemic index (LGI) or a high glycemic index (HGI), which were fed to two groups of mice for 13 weeks.

tag: gender

value: male

tag: developmental stage

value: adult

value: epididymal white adipose tissue

source_name: epididymal white adipose tissue, reference pool of all LGI and HGI samples


title: epiWAT HGI replicate 05

tag: tissue


title: Triple-negative breast cancer_024

description:
TNBC_024
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_029

description:
TNBC_029
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_026

description:
TNBC_026
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_031

description:
TNBC_031
Gene expression data from primary breast tumors.


title: epiWAT HGI replicate 09


title: Triple-negative breast cancer_025

description:
TNBC_025
Gene expression data from primary breast tumors.


title: epiWAT HGI replicate 04


title: epiWAT HGI replicate 07


title: Triple-negative breast cancer_030

description:
TNBC_030
Gene expression data from primary breast tumors.


title: epiWAT LGI replicate 09

source_name: epididymal white adipose tissue, high fat, low glycemic index diet (LGI)


title: epiWAT HGI replicate 02


title: epiWAT HGI replicate 03


title: epiWAT HGI replicate 06


title: epiWAT HGI replicate 01


title: Triple-negative breast cancer_023

description:
TNBC_023
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_022

description:
TNBC_022
Gene expression data from primary breast tumors.


title: epiWAT LGI replicate 08


title: Triple-negative breast cancer_021

description:
TNBC_021
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_020

description:
TNBC_020
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_019

description:
TNBC_019
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_017

description:
TNBC_017
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_018

description:
TNBC_018
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_016

description:
TNBC_016
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_009

description:
TNBC_009
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_010

description:
TNBC_010
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_014

description:
TNBC_014
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_012

description:
TNBC_012
Gene expression data from primary breast tumors.


title: epiWAT LGI replicate 04

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.


title: epiWAT LGI replicate 07


title: Triple-negative breast cancer_013

description:
TNBC_013
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_015

description:
TNBC_015
Gene expression data from primary breast tumors.


title: epiWAT LGI replicate 06


title: epiWAT LGI replicate 01


title: epiWAT LGI replicate 05


title: Triple-negative breast cancer_011

description:
TNBC_011
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_008

description:
TNBC_008
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_005

description:
TNBC_005
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_004

description:
TNBC_004
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_007

description:
TNBC_007
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_001

description:
TNBC_001
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_003

description:
TNBC_003
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_002

description:
TNBC_002
Gene expression data from primary breast tumors.


title: Triple-negative breast cancer_006

description:
TNBC_006
Gene expression data from primary breast tumors.


title: S. suis S2 transcriptional response to pH 5.8 vs. pH 7.2

city: Beijing

first: Ruifu

last: Yang

address: No.20, DOngdajie, Fengtai

institute: Institute of Microbiology and Epidemiology

description:
Streptococcus suis serotype 2 (SS2) is able to cause human infections ranging from superficial wounded skin infections to severe invasive infections such as meningitis and streptococcal toxic shock-like syndrome (STSLS). During its infection cycle, SS2 must acclimatize itself to pH shift. Herein, a whole-genome DNA microarray was used to investigate the global transcriptional regulation of an invasive SS2 strain grown to late-exponential phase at pH 5.8 relative to pH 7.2. The detected differentially regulated genes included those encoding virulence factors, antigenic proteins, ABC transporters and unknown functions. Our data provided a global profile of gene transcription induced by low acid stress and shed light on some unforeseen lines for further pathogenesis investigation.

This Sample represents 4 biological replicates.

hyb_protocol: For two-sample (reference vs. test) microarray hybridization, four independent bacterial cultures from each condition were prepared as biological replicates for RNA isolation. Accordingly, four dual-fluorescence-labeled cDNA probes were prepared to hybridize with four slides. Pairwise comparisons were made using dye swaps to avoid labeling bias. For hybridization, the slides were incubated in 50 µl of prehybridization buffer (5X SSC, 0.1% SDS and 0.1% BSA) at 42°C for at least 1 hr. The slides were washed twice in water for 1 min and once in 95% ethanol for 1 min, and then blown to dry with hot air. Dual-fluorescence labeled dried probes were resuspended in 35 µl of hybridization solution (50% deionized formamide, 5×SSC, 0.1% SDS, 5×Denhardt’s solution, and 0.5 µg/µl of sheared salmon sperm DNA). The mixture was denatured at 98°C for 5 min, and then was applied to the microarray slide followed by covering a 24×50 mm glass coverslip. The slides were hybridized in a moisture chamber at 42°C for 18 to 20 hr in a hybridization incubator (Robbins Scintific). After hybridization, the slides were washed in 1×SSC with 0.06% SDS for 2 min, then in 0.06×SSC for 2 min and finally in ethanol for 1 min. The slides were blown dry for scanning.

scan_protocol: The hybridized slides were scanned at a resolution of 10 µm by using a GenePix Personal 4100A Microarray Scanner (Axon Instruments). The scanned images were processed and the data were further analyzed by using GenePix Pro 5.0 software (Axon Instruments) combined with Microsoft Excel software.

data_processing: The scanned images were processed and the data were further analyzed by using GenePix Pro 5.0 software (Axon Instruments) combined with Microsoft Excel software. Spots were analyzed by adaptive quantitation, and the local background was subsequently subtracted. Spots with background-corrected signal intensity (median) in both channels less than two folds of background intensity (median) were rejected from further analysis. Data normalization was performed on the remaining spots by total intensity normalization methods with using GenePix Pro 5.0 software. The normalized log2 ratio of reference/test (pH 7.2/pH 5.8) signal for each spot was recorded. Genes with less than four data points were considered unreliable, and their data points were discarded as well. The averaged log2 ratio for each remaining gene on the four replicate slides was ultimately calculated. Significant changes of gene transcription level were identified with SAM software using one class mode. After the SAM analysis, only genes with at least 2-fold changes in expression were collected for further analysis.

organism: Streptococcus suis 05ZYH33

source_name: Streptococcus suis, reference pH 7.2

label_protocol:
For two-sample (reference versus test) microarray hybridization, four independent bacterial cultures from each condition were prepared as biological replicates for RNA isolation. Accordingly, four dual-fluorescence-labeled cDNA probes were prepared to hybridize with four slides. Pairwise comparisons were made using dye swaps to avoid labeling bias.
20 µg of total RNA was mixed with 3µg random hexamer primers, heated to 70°C for 10 min, and cooled quickly on ice. 1µl of RNasin RNase inhibitor (Promega), 8 µl of 5×reverse transcription buffer, 4 µl of 0.1 M DDT, 1.6 µl of unmodified dNTP mixture (12.5 mM of each dATP, dGTP, and dCTP, plus 7.5 mM dTTP), 2 µl of 4 mM aminoallyl-dUTP (Sigma) and 200 U of SuperScript Ⅲ reverse transcriptase (Invitrogen) were added to a final volume of 40 µl. The reaction occurred at 50°C for 1 hr, after which an additional 200 U of Superscript Ⅲ reverse transcriptase was added. The mixture was then incubated at 50°C for an additional hour. The reaction was stopped by the addition of 20 mM EDTA, and the RNA was degraded by the addition of NaOH to a final concentration of 30 mM, followed by incubation at 65°C for 15 min. The mixture was neutralized by adding HCl to a final concentration of 30 mM. Free amines were removed by using Qiaquick PCR purification columns (Qiagen). The purified cDNA was air dried at 50°C, and then labeled by the addition of 1/10 of one reaction vial of Cy3 or Cy5 monofunctional dye (Amersham) in 0.05 M sodium bicarbonate (pH9.3) and incubated for 2 hr at room temperature in the dark.

extract_protocol: Before bacterial harvest, double-volume of RNAprotect Bacteria Reagent (Qiagen) was added immediately to each cell culture. Total RNA extraction was performed by using MasterPureTM RNA Purification kits (Epicenter) as mentioned in our previous report. RNA quality was monitored by agarose gel electrophoresis and RNA quantity was measured by spectrophotometer.

tag: serotype

tag: growth phase

value: mid-exponential

tag: treatment

label: Cy5, Cy3

source_name: Streptococcus suis, test pH 5.8


title: epiWAT LGI replicate 02


title: Triple-negative breast cancer_064

description:
TNBC_064
Gene expression data from primary breast tumors.

tag: lymph node status (0

tag: grade (12


title: HeLa SGR Vs HeLa DMSO Experiment_3

status: Public on Sep 12 2011

city: Bangalore

first: Tapas

middle: Kumar

last: Kundu

state: Karnataka

address: Jakkur

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced scientific Research

description: Grid and spot alignment is performed by using Scanarray microarray analysis software form PerkinElmer.

hyb_protocol: 1. Carefully pipette entire 40 ul sample mixture onto the middle of the array surface. Do not allow direct contact of the array surface with pipette tip, as this may scratch the array surface. Avoid creation of air bubbles in the hybridization buffer. 2. Gently overlay the cover slip onto the solution on the array by positioning the cover slip at one end of the array and lowering it down until it is in contact with the hybridization solution. Be sure the solution covers the entire array footprint. Small bubbles will not to lose hybridization. 3. Pipet 500 ul of 2X SSC onto a flat, folded dust free tissue. This is sufficient to maintain the humidity inside the hybridization chamber. 4. Very carefully, place the microarray slide over the damp tissue and seal the cap tightly. Be very careful that the cover slip does not slip off. Be sure that the array does not touch the tissue as this may remove hybridization solution from the array surface through capillary action. 5. Place the tube in a 650 C incubator. Ensure the microarray, now enclosed in the tube, is level and stable in the incubator. Allow the hybridization to proceed overnight (18 hours) at this temperature.

scan_protocol: Laser detection of Cyanine 3 and Cyanine 5 fluorescence is performed using a confocal scanning instrument containing two tuned lasers, which excite Cyanine dyes at the appropriate wavelengths.

data_processing: Scan data (Raw data) is analyzed using GeneSpring GX v7.3. Per spot per chip lowess normalization was done. To account for dye swap, the signal channel and control channel measurements for sample(s) 2 were reversed. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Biological analysis was done using Genotypic's Biointerpreter software.

source_name: HeLa cell line treated with DMSO

label_protocol: Labeling of cDNA was carried out using the MICROMAXTM Direct Labeling Kit (PerkinElmer Life Sciences) according to the manufacturer’s instructions. Typically, 40 µg total RNA was used in each of the labeling reactions

extract_protocol: Trizol Method

tag: cell line

value: HeLa

value: derived from human cervical cancer tissue

value: DMSO

source_name: HeLa cell line treated with SGR

label_protocol: Labeling of cDNA was carried out using the MICROMAXTM Direct Labeling Kit (PerkinElmer Life Sciences) according to the manufacturer’s instructions. Typically, 50 µg total RNA was used in each of the labeling reactions.

value: sanguinarine (SGR)


title: HeLa SGR Vs HeLa DMSO Experiment_1


title: HeLa DMSO Vs HeLa SGR Experiment_1


title: HeLa DMSO Vs HeLa SGR Experiment_2


title: TF1_Mock_rep3

city: Tokyo

first: Aiko

last: Sato-Otsubo

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

hyb_protocol: Affymetrix starndard

scan_protocol: Affymetrix starndard

data_processing: Raw array signals were processed using Expression Console software (Affymetrix) in which RMA was performed.

source_name: TF1 cells, mock

label_protocol: Affymetrix starndard

growth_protocol: HeLa and TF-1 cells were retrovirally transduced with either mock, wild-type U2AF35 or S34F mutant . The cells were sorted by GFP-marking using a MoFlo® FACS cell sorter (Beckman Coulter) 48 hrs after retoroviral tranduction.

extract_protocol: Total RNA from cultured cells was isolated with the RNeasy Total RNA kit (Qiagen) using RNase-free DNase set (Qiagen) to reduce contamination of genomic DNA according to the manufacturer’s protocol.

tag: transduction

value: mock


title: TF1_WT_rep3

source_name: TF1 cells, wild-type U2AF35

value: wild-type U2AF35


title: TF1_WT_rep1


title: HeLa_S34F_rep2

source_name: HeLa cells, S34F U2AF35

value: S34F U2AF35


title: TF1_Mock_rep1


title: TF1_S34F_rep1

source_name: TF1 cells, S34F U2AF35


title: TF1_WT_rep2


title: HeLa_S34F_rep1


title: HeLa_WT_rep3

source_name: HeLa cells, wild-type U2AF35


title: TF1_Mock_rep2


title: HeLa_S34F_rep3


title: TF1_S34F_rep3


title: HeLa_WT_rep1


title: HeLa_WT_rep2