title: BDF1_4-cell_2

city: Tsukuba

first: Kimiko

last: Inoue

state: Ibaraki

address: 3-1-1 Koyadai

department: Bioresource Engineering Division

country: Japan

institute: BRC, RIKEN

description: Gene expression in (B6xDBA/2)F1 4-cell blastomere transferred blastocyst

hyb_protocol: 1.65μg Cy3 labelled RNA was hybridized to a whole mouse genome oligo DNA microarray (4 × 44K, Agilent Technologies) for 16 h at 65°C using Gene Expression Hybridization kit (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: Scanning of microarray slides was performed with a DNA microarray scanner at a 5 μm resolution (Agilent Technologies).

data_processing: Scanned image files were processed to give signal intensities using Feature Extraction software (Agilent Technologies, version 9.5.3.1). All raw data were loaded into Gene Spring GX 7.3 software (Agilent Technologies) and a per chip normalization to the 50th percentile was performed.

source_name: 4-cell blastomere clone, 96h cultured, replicate2

label_protocol: 5μg amplified aminoallyl RNA was coupled with Cy3 dye (GE Healthcare) for 1.5 h and eluted with RNeasy Mini kit (QIAGEN). Yield of Cy3 labelled RNA was measured by Nano Drop ND-1000 (Thermo Scientific).

growth_protocol: In vitro fertilized or cloned embryos were cultured with KSOM for 96 h at 37°C in a humidified atmosphere containing 6.0% CO2.

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) from single IVF or cloned blastocysts cultured for 96 h. RNA from a single blastocyst was subjected to two rounds of linear amplification using TargetAmp Two-Round Aminoallyl-aRNA Amplification Kits (Epicentre) according to the manufacturer’s instructions.

tag: sex

value: female


title: CZ28_GWP

status: Public on Sep 17 2010

type: genomic

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CZ28

hyb_protocol: Following fragmentation, 90 micrograms of biotin-labeled DNA were hybridized for 16 hr at 49°C on GeneChip Human Mapping 250K NspI Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Human Mapping 250K NspI arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Images were acquired using Affymetrix GeneChip Operating System (GCOS 1.4). The raw data for individual SNPs were extracted from CEL files and converted into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares using the Hidden Markov Model algorithm with a genomic smoothing window set to 0. After the pre-processing, piecewise constant estimates of the underlying local DNA copy number (CN) variation was calculated using the DNAcopy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS), (Olshen et al., Biostatistics 2004) and the median of the estimated profiles was scaled back to a nominal multiplicity of two. After scaling, a k-means clustering algorithm was used on the cumulative profile of all the data to determine the thresholds for inferring discrete CN values. Inferred CN higher than 2.1 and 2.5 corresponded to gain and amplification whereas CN below 1.9 and 1.34 to loss and biallelic deletion, respectively.

The pre-processed data generated by GTYPE/CNAT are available in 'GSE16746_CNAT_signals.txt', which is linked to the Series GSE16746 record as a supplementary file.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Human B-cell chronic lymphocytic leukemia patient CZ28

label_protocol: Biotinylated DNA were prepared according to the standard Affymetrix protocol starting from 250 nanograms of genomic DNA.

extract_protocol: Genomic DNA extraction was performed using the Wizard Genomic DNA Purification kit according to the manufacturer's instructions (Promega).

treatment_protocol: Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque (Seromed, Biochrom KG, Berlin, Germany) density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer (Becton Dickinson & Co, Sunnyvale, CA) with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome (Becton Dickinson). If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody (mAb) treatment (Becton Dickinson) followed by magnetic beads (Goat Anti-Mouse IgG Dynabeads, Dynal Biotech ASA, Oslo, Norway).

tag: legend

value: VH status = IgVH mutational status (Fais et al. J Clin Invest, 1998)

tag: Sex

value: M

tag: vh status

value: mut

tag: disease

value: B-cell chronic lymphocytic leukemia (B-CLL)

tag: Stage

value: Binet A

tag: cell type

value: CD5/CD19/CD23 triple-positive B cells


title: B6x129_IVF_1

status: Public on Sep 16 2010

type: RNA

description: Gene expression in (B6x129/Sv-ter)F1 in vitro fertilized blastocyst

molecule: total RNA

organism: Mus musculus

source_name: in vitro fertilized, 96h cultured, replicate1

tag: strain


title: BDF1_4-cell_1

source_name: 4-cell blastomere clone, 96h cultured, replicate1

value: male


title: B6x129_IVF_2

source_name: in vitro fertilized, 96h cultured, replicate2


title: B6x129_sc_1

description: Gene expression in (B6x129/Sv-ter)F1 somatic cell nuclear transferred blastocyst

source_name: Sertoli cell clone, 96h cultured, replicate1


title: CZ4_GWP

description: Genome-wide profiling data from human B-cell chronic lymphocytic leukemia patient CZ4

source_name: Human B-cell chronic lymphocytic leukemia patient CZ4


title: B6x129_sc_2

source_name: Sertoli cell clone, 96h cultured, replicate2


title: Estradiol  only- Rep 1

city: Brisbane

first: Ashkan

last: Amirshahi

state: QLD

address: 60 Musk ave, Kelvin Grove

department: Infectious diseases

country: Australia

institute: Institute of Health and Biomedical Innovation (IHBI)

description: Human Endometrial cancer cells (ECC-1) were infected with the human pathogen Chlamydia trachomatis serovar D, in the presence or absence of human female reproductive hormones estradiol and progesterone. The bacterial gene expression levels were examined 48 hours post-infection

hyb_protocol: Hybridisation, blocking and washing protocols identical to the E.coli hybridization protocols were used to facilitate binding of the labelled chlamydial transcripts.

scan_protocol: Standard scan protocol as per the E.coli genome array was applied when scanning the custom Chlamydia array.

data_processing:
The matrix table was generated through Affymetrix’s GCOS software version 1.4, normalised and the resultant data was exported into a Microsoft Excel spreadsheet for further processing. Default parameters for the software was used.
- The fold change calculations were performed using normalised log2 ratio between the hormone-variant and non-hormone treated cell lines.

organism: Chlamydia trachomatis

source_name: Chlamydia trachomatis Serovar D supplemented with etradiol

label_protocol: Target labelling was facilitated using Affymetrix’s Prokaryotic Target Preparation, protocol as outlined in the Expression Analysis Technical Manual

growth_protocol: The hormone-responsive human endometrial cell line ECC-1 was cultured for 24 hours in physiological concentrations of estradiol and/or progesterone, and then infected with C. trachomatis serovar D at a Multipilicity of Infection (MOI) of 15. All cell lines were pre-treated in activated charcoal medium (name) for 26 weeks prior to the addition of the female reproductive hormones and Chlamydia trachomatis serovar D.

extract_protocol: For the extraction of prokaryotic messenger RNA, a Trizol (Invitrogen) protocol following the manufacturer’s instructions was used for total RNA, followed by Dynabead purification (poly A+ purification kit)  (Dynal Biotech ASA, Oslo, Norway) for isolation of prokaryotic RNA.

treatment_protocol: Average physiological concentrations of 17β-estradiol, progesterone, and a combination of 17β-estradiol and progesterone (1:1) were added to respective wells once cells have reached full confluence, and supplemented with hormones continuously for 24 hours prior to infection. Although the physiological concentration of progesterone is higher than estradiol, in this study a combination of 1:1, estradiol and progesterone, was chosen as starting point to merely determine the effect of both hormones together.

tag: serovar

tag: cell line


title: BDF1_tt_8

description: Gene expression in (B6xDBA/2)F1 somatic cell nuclear transferred blastocyst

source_name: fibroblast clone, 96h cultured, replicate8


title: BDF1_4-cell_3

source_name: 4-cell blastomere clone, 96h cultured, replicate3


title: BDF1_tt_7

source_name: fibroblast clone, 96h cultured, replicate7


title: Progesterone only-Rep1

source_name: Chlamydia trachomatis Serovar D supplemented with progesterone

value: Human Endometrial cancer cells (ECC-1) were infected with the human pathogen Chlamydia trachomatis serovar D


title: B6x129_sc_4

source_name: Sertoli cell clone, 96h cultured, replicate4


title: B6x129_IVF_4

source_name: in vitro fertilized, 96h cultured, replicate4


title: BDF1_tt_3

source_name: fibroblast clone, 96h cultured, replicate3


title: B6x129_sc_3

source_name: Sertoli cell clone, 96h cultured, replicate3


title: BDF1_tt_5

source_name: fibroblast clone, 96h cultured, replicate5


title: BDF1_sc_Xist_1

source_name: Sertoli cell clone, 96h cultured, Xist KO, replicate1


title: B6x129_IVF_3

source_name: in vitro fertilized, 96h cultured, replicate3


title: BDF1_tt_6

source_name: fibroblast clone, 96h cultured, replicate6


title: BDF1_tt_2

source_name: fibroblast clone, 96h cultured, replicate2


title: BDF1_sc_Xist_3

source_name: Sertoli cell clone, 96h cultured, Xist KO, replicate3


title: BDF1_sc_Xist_4

source_name: Sertoli cell clone, 96h cultured, Xist KO, replicate4


title: BDF1_sc_Xist_2

source_name: Sertoli cell clone, 96h cultured, Xist KO, replicate2


title: BDF1_cc_Xist_5

source_name: cumulus cell clone, 96h cultured, Xist KO, replicate5


title: BDF1_cc_Xist_4

source_name: cumulus cell clone, 96h cultured, Xist KO, replicate4


title: BDF1_cc_Xist_1

source_name: cumulus cell clone, 96h cultured, Xist KO, replicate1


title: BDF1_cc_Xist_2

source_name: cumulus cell clone, 96h cultured, Xist KO, replicate2


title: Progesterone only-Rep2

source_name: Chlamydia trachomatis Serovar D supplemented with progesterone


title: BDF1_cc_Xist_3

source_name: cumulus cell clone, 96h cultured, Xist KO, replicate3


title: BDF1_sc_4

source_name: Sertoli cell clone, 96h cultured, replicate4


title: BDF1_sc_2

source_name: Sertoli cell clone, 96h cultured, replicate2


title: CCRF-CEM cells, healthy control sera, rep1

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

country: USA

institute: Medical College of Wisconsin

description:
Gene expression data from cell lines stimulated with RO or HC sera.
CCRF-CEM_HC1
Biological replicate 1 of 3.

hyb_protocol: The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.

scan_protocol: Arrays were scanned with a 7G Affymetrix GeneChip Scanner.

data_processing: Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals.  Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total).  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.

source_name: CCRF-CEM cells stimulated with healthy-control sera

label_protocol: cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin.  Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician.  Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.

extract_protocol: Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA).  These were selected on the basis of their original cell type, properties and characteristics.  Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma.  After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).

value: CCRF-CEM

tag: treatment

value: health control sera


title: CCRF-CEM cells, healthy control sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
CCRF-CEM_HC2
Biological replicate 2 of 3.


title: BDF1_sc_3

source_name: Sertoli cell clone, 96h cultured, replicate3


title: CCRF-CEM cells, recent-onset type I diabetes sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
CCRF-CEM_RO2
Biological replicate 2 of 3.

source_name: CCRF-CEM cells stimulated with recent-onset type I diabetes sera

value: recent-onset type I diabetes sera


title: BDF1_sc_1

source_name: Sertoli cell clone, 96h cultured, replicate1


title: CCRF-CEM cells, recent-onset type I diabetes sera, rep1

description:
Gene expression data from cell lines stimulated with RO or HC sera.
CCRF-CEM_RO1
Biological replicate 1 of 3.


title: HL-60 cells, healthy control sera, rep1

description:
Gene expression data from cell lines stimulated with RO or HC sera.
HL-60_HC1
Biological replicate 1 of 3.

source_name: HL-60 cells stimulated with healthy-control sera


title: CCRF-CEM cells, recent-onset type I diabetes sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
CCRF-CEM_RO3
Biological replicate 3 of 3.


title: HL-60 cells, recent-onset type I diabetes sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
HL-60_RO3
Biological replicate 3 of 3.

source_name: HL-60 cells stimulated with recent-onset type I diabetes sera


title: HL-60 cells, healthy control sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
HL-60_HC2
Biological replicate 2 of 3.


title: BDF1_tt_1

source_name: fibroblast clone, 96h cultured, replicate1


title: IM9 cells, healthy control sera, rep1

description:
Gene expression data from cell lines stimulated with RO or HC sera.
IM9_HC1
Biological replicate 1 of 3.

source_name: IM9 cells stimulated with healthy-control sera


title: IM9 cells, healthy control sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
IM9_HC3
Biological replicate 3 of 3.


title: BDF1_cc_6

source_name: cumulus cell clone, 96h cultured, replicate6


title: BDF1_cc_TSA_2

source_name: cumulus cell clone, 96h cultured, TSA treated, replicate2


title: BDF1_cc_2

source_name: cumulus cell clone, 96h cultured, replicate2


title: IM9 cells, healthy control sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
IM9_HC2
Biological replicate 2 of 3.


title: BDF1_cc_7

source_name: cumulus cell clone, 96h cultured, replicate7


title: HL-60 cells, healthy control sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
HL-60_HC3
Biological replicate 3 of 3.


title: BDF1_cc_TSA_3

source_name: cumulus cell clone, 96h cultured, TSA treated, replicate3


title: BDF1_cc_3

source_name: cumulus cell clone, 96h cultured, replicate3


title: BDF1_tt_4

source_name: fibroblast clone, 96h cultured, replicate4


title: HL-60 cells, recent-onset type I diabetes sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
HL-60_RO2
Biological replicate 2 of 3.


title: BDF1_cc_1

source_name: cumulus cell clone, 96h cultured, replicate1


title: HL-60 cells, recent-onset type I diabetes sera, rep1

description:
Gene expression data from cell lines stimulated with RO or HC sera.
HL-60_RO1
Biological replicate 1 of 3.


title: IM9 cells, recent-onset type I diabetes sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
IM9_RO3
Biological replicate 3 of 3.

source_name: IM9 cells stimulated with recent-onset type I diabetes sera


title: BDF1_cc_5

source_name: cumulus cell clone, 96h cultured, replicate5


title: BDF1_cc_TSA_1

source_name: cumulus cell clone, 96h cultured, TSA treated, replicate1


title: CCRF-CEM cells, healthy control sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
CCRF-CEM_HC3
Biological replicate 3 of 3.

source_name: CCRF-CEM cells stimulated with healthy-control sera


title: K562 cells, healthy control sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
K562_HC3
Biological replicate 3 of 3.

source_name: K562 cells stimulated with healthy-control sera


title: K562 cells, recent-onset type I diabetes sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
K562_RO3
Biological replicate 3 of 3.

source_name: K562 cells stimulated with recent-onset type I diabetes sera


title: BDF1_IVF_12

description: Gene expression in (B6xDBA/2)F1 in vitro fertilized blastocyst

source_name: in vitro fertilized, 96h cultured, replicate12


title: BDF1_IVF_11

source_name: in vitro fertilized, 96h cultured, replicate11


title: IM9 cells, recent-onset type I diabetes sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
IM9_RO2
Biological replicate 2 of 3.


title: BDF1_IVF_8

source_name: in vitro fertilized, 96h cultured, replicate8


title: BDF1_cc_4

description: Gene expression in (B6xDBA/2)F1 somatic cell nuclear transferred blastocyst

source_name: cumulus cell clone, 96h cultured, replicate4


title: BDF1_IVF_7

source_name: in vitro fertilized, 96h cultured, replicate7


title: BDF1_IVF_1

source_name: in vitro fertilized, 96h cultured, replicate1


title: BDF1_IVF_4

source_name: in vitro fertilized, 96h cultured, replicate4


title: BDF1_IVF_5

source_name: in vitro fertilized, 96h cultured, replicate5


title: K562 cells, recent-onset type I diabetes sera, rep1

description:
Gene expression data from cell lines stimulated with RO or HC sera.
K562_RO1
Biological replicate 1 of 3.


title: BDF1_IVF_9

source_name: in vitro fertilized, 96h cultured, replicate9


title: BDF1_IVF_3

source_name: in vitro fertilized, 96h cultured, replicate3


title: K562 cells, healthy control sera, rep1

description:
Gene expression data from cell lines stimulated with RO or HC sera.
K562_HC1
Biological replicate 1 of 3.


title: THP-1 cells, healthy control sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
THP-1_HC3
Biological replicate 3 of 3.

source_name: THP-1 cells stimulated with healthy-control sera


title: BDF1_IVF_2

source_name: in vitro fertilized, 96h cultured, replicate2


title: BDF1_IVF_10

source_name: in vitro fertilized, 96h cultured, replicate10


title: BDF1_IVF_6

source_name: in vitro fertilized, 96h cultured, replicate6


title: KG-1 cells, healthy control sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
KG-1_HC3
Biological replicate 3 of 3.

source_name: KG1 cells stimulated with healthy-control sera


title: IM9 cells, recent-onset type I diabetes sera, rep1

description:
Gene expression data from cell lines stimulated with RO or HC sera.
IM9_RO1
Biological replicate 1 of 3.

source_name: IM9 cells stimulated with recent-onset type I diabetes sera


title: KG-1 cells, recent-onset type I diabetes sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
KG-1_RO2
Biological replicate 2 of 3.

source_name: KG1 cells stimulated with recent-onset type I diabetes sera


title: KG-1 cells, recent-onset type I diabetes sera, rep1

description:
Gene expression data from cell lines stimulated with RO or HC sera.
KG-1_RO1
Biological replicate 1 of 3.


title: KG-1 cells, healthy control sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
KG-1_HC2
Biological replicate 2 of 3.


title: THP-1 cells, recent-onset type I diabetes sera, rep1

description:
Gene expression data from cell lines stimulated with RO or HC sera.
THP-1_RO1
Biological replicate 1 of 3.

source_name: THP-1 cells stimulated with recent-onset type I diabetes sera


title: THP-1 cells, healthy control sera, rep1

description:
Gene expression data from cell lines stimulated with RO or HC sera.
THP-1_HC1
Biological replicate 1 of 3.


title: K562 cells, healthy control sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
K562_HC2
Biological replicate 2 of 3.

source_name: K562 cells stimulated with healthy-control sera


title: KG-1 cells, recent-onset type I diabetes sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
KG-1_RO3
Biological replicate 3 of 3.


title: K562 cells, recent-onset type I diabetes sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
K562_RO2
Biological replicate 2 of 3.

source_name: K562 cells stimulated with recent-onset type I diabetes sera


title: U-937 cells, healthy control sera, rep1

description:
Gene expression data from cell lines stimulated with RO or HC sera.
U-937_HC1
Biological replicate 1 of 3.

source_name: U-937 cells stimulated with healthy-control sera


title: U-937 cells, healthy control sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
U-937_HC2
Biological replicate 2 of 3.


title: THP-1 cells, recent-onset type I diabetes sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
THP-1_RO2
Biological replicate 2 of 3.


title: THP-1 cells, healthy control sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
THP-1_HC2
Biological replicate 2 of 3.


title: THP-1 cells, recent-onset type I diabetes sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
THP-1_RO3
Biological replicate 3 of 3.


title: KG-1 cells, healthy control sera, rep1

description:
Gene expression data from cell lines stimulated with RO or HC sera.
KG-1_HC1
Biological replicate 1 of 3.


title: U-937 cells, healthy control sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
U-937_HC3
Biological replicate 3 of 3.


title: U-937 cells, recent-onset type I diabetes sera, rep3

description:
Gene expression data from cell lines stimulated with RO or HC sera.
U-937_RO3
Biological replicate 3 of 3.

source_name: U-937 cells stimulated with recent-onset type I diabetes sera


title: U-937 cells, recent-onset type I diabetes sera, rep2

description:
Gene expression data from cell lines stimulated with RO or HC sera.
U-937_RO2
Biological replicate 2 of 3.


title: U-937 cells, recent-onset type I diabetes sera, rep1

description:
Gene expression data from cell lines stimulated with RO or HC sera.
U-937_RO1
Biological replicate 1 of 3.


title: mock, 48 hr, rep 3

city: Columbia

first: Marc

last: Libault

state: MO

address: 1201 Rollins Street

department: Plant Sciences

institute: University of Missouri

description:
C_48_3
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

hyb_protocol: Purified, fragmented cRNA was hybridized to Affymetrix's Soybean Genome Array using Affymetrix's GeneChip Fluidics Station 450, as per Affymetrix's instructions.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Pre-processing was done separately for two groups: 1) all 6, 12 and 18 hr samples, and 2) all 24, 36 and 48 hr samples. For both groups, only the 37,641 soybean probe sets on the array were used for normalization, computed using the GCRMA algorithm using the R 2.7 and Bioconductor packages.

organism: Glycine max

source_name: root hair cells, mock, 48 hr

label_protocol: Biotin-labeled cRNA samples were made using Affymetrix GeneChip  Expression 3'-Amplification Reagents (One-Cycle Target Labeling and Control Reagents package) according to the manufacturer's instructions.

growth_protocol: Soybean (Glycine max) seeds were surface sterilized according to Wan et al. (2005) (PMID: 15915644) and then placed on nitrogen-free B&D agar medium (Broughton andDilworth, 1971) in growth chambers (dark conditions, 80% humidity, 27 C).

extract_protocol: Total RNA were extracted from the isolated root hair cells using Trizol (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: After 3 d of germination in growth chambers, a B. japonicum cell suspension or water (mock inoculation) was sprayed on approximately 2,000 seedlings growing on B&D agar medium. Treated seedlings were returned to the original growth chamber for incubation. Root hair cells were isolated according to Wan et al. (2005).

tag: cultivar

value: Williams 82

tag: tissue

value: root hair cells from seedlings

tag: treatment age

value: 3 days post-germination

value: mock-inoculated by water

tag: time

value: 48 hr post-inoculation


title: mock, 36 hr, rep 3

description:
C_36_3
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

source_name: root hair cells, mock, 36 hr

value: 36 hr post-inoculation


title: mock, 24 hr, rep 3

description:
C_24_3
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

source_name: root hair cells, mock, 24 hr

value: 24 hr post-inoculation


title: inoculated, 36 hr, rep 2

description:
Bj_36_2
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

source_name: root hair cells, inoculated, 36 hr

value: inoculated by Bradyrhizobium japonicum USDA110


title: inoculated, 24 hr, rep 2

description:
Bj_24_2
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

source_name: root hair cells, inoculated, 24 hr


title: inoculated, 36 hr, rep 3

description:
Bj_36_3
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: inoculated, 48 hr, rep 3

description:
Bj_48_3
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

source_name: root hair cells, inoculated, 48 hr


title: mock, 48 hr, rep 2

description:
C_48_2
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: inoculated, 48 hr, rep 1

description:
Bj_48_1
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: mock, 36 hr, rep 2

description:
C_36_2
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: mock, 24 hr, rep 2

description:
C_24_2
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: inoculated, 48 hr, rep 2

description:
Bj_48_2
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: CD8+_effector_rep4

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: Agilent Technologies (Santa Clara, CA) following manufacturer’s protocol.

data_processing: Background correction was based on a local background estimate and spatial detrending. The default Agilent normalization procedure, called Linear & Lowess, was applied. Exact protocol and parameter settings are described in the Agilent Feature Extraction Software User Manual 7.5.

source_name: CD8+ T cells, effector

label_protocol: Dye coupling reaction (Amersham, England)

extract_protocol: Nucleospin RNA isolation kit (Machery-Nagel, Düren, Germany)

treatment_protocol: Ex vivo isolated CD8+ T cells

value: CD8+ T cells

tag: type

tag: donor

value: pool of donor 4,5,6

source_name: CD8+ T cells, naive

value: pool of donor 1-6


title: inoculated, 24 hr, rep 3

description:
Bj_24_3
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: CD8+_effector_rep2

scan_protocol: Agilent Technologies (Santa Clara, CA) following manufacturer’s protocol.

value: donor 2


title: CD8+_memory_rep2

source_name: CD8+ T cells, memory


title: mock, 36 hr, rep 1

description:
C_36_1
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: CD8+_effector_rep3

value: donor 3


title: inoculated, 36 hr, rep 1

description:
Bj_36_1
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: CD8+_memory_rep3


title: CD8+_memory_rep1

value: donor 1


title: CD8+_memory_rep4


title: CD8+_effector_rep1


title: mock, 24 hr, rep 1

description:
C_24_1
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: CD8+_naive_rep3


title: inoculated, 24 hr, rep 1

description:
Bj_24_1
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: CD8+_naive_rep2


title: FY4 vs Sigma1278b, biological replicate 1

city: Cambridge

first: Alex

last: Rolfe

state: MA

address: 77 Massachusetts Ave, 32-G538

department: CSAIL

institute: Massachusetts Institute of Technology

description: biological replicate 1 (ExTaq, Cy labeling)

hyb_protocol: Apply DNA to array such that equamolar amounts of each dye (between 40 and 100 pMol) are applied to the array.   Use Agilent's genomic DNA (CGH) protocols for hybridization (40hrs at 65C) and washing.

scan_protocol: Scanned on an Agilent Technologies Scanner model G2505B and feature intensities extracted using Agilent's feature extraction software (v9.5.3.1) and no normalization.

data_processing:
Unnormalized Cy5 and Cy3 values from the feature extracted file were loaded into our database for further normalization to (1) adjust Cy3 values by a multiplicative factor such that the median Cy3 intensity was equal to the medial Cy5 intensity and (2) a rotational normalization such that the best fit line via linear regression falls along Cy5=Cy3.
Attached 'sigma.ecori' supplementary file contains the normalized data after probe mapping. The columns are chromosome, position, strand, cy5, cy3.

organism: Saccharomyces cerevisiae

label_protocol: See extended protocol in http://cgs.csail.mit.edu/rulers/protocol.doc

growth_protocol: Grow one liter of yeast to an OD600 of roughly 1.0.  This will give ~ 3x10^10 yeast cells.

extract_protocol: Pellet yeast cells and store at –80 until you are ready to isolate the DNA. Thaw Pellets. Resuspend 3x10^10 cells in 12 ml TE.  Pellet for 5 minutes at 3000RPM 4 degrees.  Remove supernatant.  The rest of the DNA prep is a variation of Qiagen 250 DNA prep kit.


title: FY4 vs Sigma1278b, biological replicate 2

description: biological replicate 2 (Vent Exo-, Amino Allyl labeling)


title: Rat_Lung_5wk_Trp-deficient_biological rep5

city: Bethesda

first: Julian

middle: CK

last: Lui

state: MD

address: 10 Center Drive

institute: NICHD, NIH

description: Gene expression data from Trp-deficient 5-wk-old rat lung.

hyb_protocol: cRNA were hybridized on Affymetrix Rat Genome 230 2.0 Array GeneChips according to standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to standard Affymetrix protocol.

data_processing: The data were analyzed with the Affymetrix Microarray Suite version 5.0 (MAS 5.0) algorithm.

organism: Rattus norvegicus

source_name: Lung isolated from 5-wk-old rat that was tryptophan-deficient from birth to 4wk

label_protocol: 2 ug RNA was labeled with biotin according to the standard Affymetrix protocol.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA, USA) followed by RNeasy Mini Kit purification (Qiagen, Valencia, CA, USA).

treatment_protocol: Rats were fed a tryptophan-deficient diet from birth to 4 weeks.

value: Sprague-Dawley

value: whole lung

tag: genotype

value: wild-type

tag: age

value: 35 days old

tag: diet

value: tryptophan-deficient


title: Rat_Lung_5wk_Trp-deficient_biological rep4


title: CD8+_naive_rep4


title: CD8+_naive_rep1


title: Rat_Lung_5wk_Trp-deficient_biological rep3


title: mock, 18 hr, rep 4

description:
H2O_18_4
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

source_name: root hair cells, mock, 18 hr

value: Williams 82

value: root hair cells from seedlings

value: 3 days post-germination

value: 18 hr post-inoculation


title: inoculated, 18 hr, rep 4

description:
BW_18_4
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

source_name: root hair cells, inoculated, 18 hr


title: 316_xylem_rep2

city: Gainesville

first: Leandro

middle: Gomide

last: Neves

state: FL

address: 2033 Mowry Road

department: Plant Molecular and Cell Biology

institute: University of Florida

description: Biological repetition 2 of genotype 316

hyb_protocol: Samples were hybridized at the Interdisciplinary Center for Biotechnology Research (ICBR) of the University of Florida following Agilent’s protocol, except for lowering the hybridization temperature to 55 oC to compensate for the shorter probes.

scan_protocol: As described elsewhere (http://www.chem.agilent.com/Library/usermanuals/Public/G2566-90017.pdf)

data_processing: The raw median signal intensity for each probe was log2 transformed and quantile-normalized using the Affy package on R.

organism: Eucalyptus grandis x Eucalyptus urophylla

source_name: Eucalyptus grandis X Eucalyptus urophylla segregationg population; xylem tissue

label_protocol: The Two-Color Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) was used to synthesize complementary RNA (cRNA) from 1ug of total RNA. Manufacturer’s protocol was followed except for dividing all reagents’ volume by two.

growth_protocol: Tissue was collected from field-grown, four-and-a-half-year-old trees maintained under operational silvicultural conditions in South of Brazil (Rio Grande do Sul State).

extract_protocol: Total RNA extracted (Chang et al. 1993) from xylem tissue samples was treated with RQ1 RNase-free DNase (Promega, Madison, WI, USA), purified in mini spin columns (RNeasy Plant Mini Kit, Qiagen) and had the quality visually checked on agarose gel.

treatment_protocol: None.

value: xylem from field grown trees

tag: individual


title: 305_xylem_rep2

description: Biological repetition 2 of genotype 305


title: mock, 18 hr, rep 2

description:
H2O_18_2
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

value: mock-inoculated by water


title: Rat_Kidney_5wk_Trp-deficient_biological rep3

description: Gene expression data from Trp-deficient 5-wk-old rat kidney.

source_name: Kidney isolated from 5-wk-old rat that was tryptophan-deficient from birth to 4wk

value: whole kidney


title: mock, 18 hr, rep 3

description:
H2O_18_3
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: 299_xylem_rep2

description: Biological repetition 2 of genotype 299


title: mock, 18 hr, rep 1

description:
H2O_18_1
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: Rat_Kidney_5wk_Trp-deficient_biological rep5


title: Rat_Kidney_5wk_Trp-deficient_biological rep4


title: 259_xylem_rep2

description: Biological repetition 2 of genotype 259


title: 196_xylem_rep2

description: Biological repetition 2 of genotype 196


title: 226_xylem_rep2

description: Biological repetition 2 of genotype 226


title: inoculated, 18 hr, rep 1

description:
BW_18_1
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

value: inoculated by Bradyrhizobium japonicum USDA110


title: 199_xylem_rep2

description: Biological repetition 2 of genotype 199


title: mock, 12 hr, rep 4

description:
H2O_12_4
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

source_name: root hair cells, mock, 12 hr

value: 12 hr post-inoculation


title: inoculated, 18 hr, rep 2

description:
BW_18_2
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: Rat_Kidney_5wk_Trp-deficient_biological rep1


title: 225_xylem_rep2

description: Biological repetition 2 of genotype 225


title: 214_xylem_rep2

description: Biological repetition 2 of genotype 214


title: 306_xylem_rep2

description: Biological repetition 2 of genotype 306


title: Rat_Lung_5wk_Trp-deficient_biological rep1


title: inoculated, 18 hr, rep 3

description:
BW_18_3
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: Rat_Lung_5wk_biological rep4

description: Gene expression data from control 5-wk-old rat lung.

source_name: Lung isolated from 5-wk-old rat

value: normal


title: Rat_Lung_5wk_Trp-deficient_biological rep2


title: mock, 48 hr, rep 1

description:
C_48_1
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

value: 48 hr post-inoculation


title: Rat_Lung_5wk_biological rep3


title: Rat_Lung_5wk_biological rep2


title: inoculated, 12 hr, rep 3

description:
BW_12_3
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

source_name: root hair cells, inoculated, 12 hr


title: 195_xylem_rep2

description: Biological repetition 2 of genotype 195


title: 313_xylem_rep2

description: Biological repetition 2 of genotype 313


title: inoculated, 12 hr, rep 4

description:
BW_12_4
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: mock, 12 hr, rep 3

description:
H2O_12_3
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: Rat_Kidney_5wk_Trp-deficient_biological rep2


title: 307_xylem_rep2

description: Biological repetition 2 of genotype 307


title: 218_xylem_rep2

description: Biological repetition 2 of genotype 218


title: 110_xylem_rep2

description: Biological repetition 2 of genotype 110


title: Rat_Lung_5wk_biological rep5


title: 188_xylem_rep2

description: Biological repetition 2 of genotype 188


title: Rat_Kidney_5wk_biological rep5

description: Gene expression data from control 5-wk-old rat kidney.

source_name: Kidney isolated from 5-wk-old rat


title: 212_xylem_rep2

description: Biological repetition 2 of genotype 212


title: mock, 12 hr, rep 2

description:
H2O_12_2
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: Rat_Kidney_5wk_biological rep3


title: Rat_Kidney_5wk_biological rep2


title: inoculated, 12 hr, rep 1

description:
BW_12_1
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: inoculated, 12 hr, rep 2

description:
BW_12_2
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: 114_xylem_rep2

description: Biological repetition 2 of genotype 114


title: inoculated, 6 hr, rep 4

description:
BW_6_4
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

source_name: root hair cells, inoculated, 6 hr

value: 6 hr post-inoculation


title: mock, 6 hr, rep 4

description:
H2O_6_4
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

source_name: root hair cells, mock, 6 hr


title: Rat_Lung_5wk_biological rep1

value: Sprague-Dawley


title: 96_xylem_rep2

description: Biological repetition 2 of genotype 96


title: 200_xylem_rep2

description: Biological repetition 2 of genotype 200


title: mock, 12 hr, rep 1

description:
H2O_12_1
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: 88_xylem_rep2

description: Biological repetition 2 of genotype 88


title: 93_xylem_rep2

description: Biological repetition 2 of genotype 93


title: Rat_Kidney_5wk_biological rep4


title: mock, 6 hr, rep 3

description:
H2O_6_3
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: Rat_Lung_1wk_biological rep5

description: Gene expression data from 1-wk-old rat lung.

source_name: Lung isolated from 1-wk-old rat

value: whole lung

value: 7 days old


title: Rat_Kidney_5wk_biological rep1

value: wild-type

value: 35 days old


title: 109_xylem_rep2

description: Biological repetition 2 of genotype 109


title: 81_xylem_rep2

description: Biological repetition 2 of genotype 81


title: 92_xylem_rep2

description: Biological repetition 2 of genotype 92


title: 305_xylem_rep1

description: Biological repetition 1 of genotype 305


title: 101_xylem_rep2

description: Biological repetition 2 of genotype 101


title: 259_xylem_rep1

description: Biological repetition 1 of genotype 259


title: 306_xylem_rep1

description: Biological repetition 1 of genotype 306


title: 23_xylem_rep2

description: Biological repetition 2 of genotype 23


title: 316_xylem_rep1

description: Biological repetition 1 of genotype 316


title: 307_xylem_rep1

description: Biological repetition 1 of genotype 307


title: 76_xylem_rep2

description: Biological repetition 2 of genotype 76


title: 299_xylem_rep1

description: Biological repetition 1 of genotype 299


title: 313_xylem_rep1

description: Biological repetition 1 of genotype 313


title: inoculated, 6 hr, rep 3

description:
BW_6_3
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

value: Williams 82


title: Rat_Lung_1wk_biological rep2


title: mock, 6 hr, rep 2

description:
H2O_6_2
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

value: root hair cells from seedlings


title: Rat_Lung_1wk_biological rep4


title: 225_xylem_rep1

description: Biological repetition 1 of genotype 225


title: inoculated, 6 hr, rep 2

description:
BW_6_2
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.

value: 3 days post-germination


title: Rat_Lung_1wk_biological rep1


title: 226_xylem_rep1

description: Biological repetition 1 of genotype 226


title: 212_xylem_rep1

description: Biological repetition 1 of genotype 212


title: mock, 6 hr, rep 1

description:
H2O_6_1
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: inoculated, 6 hr, rep 1

description:
BW_6_1
Gene expression data from soybean root hair cells isolated from Glycine max [L.] Merrill cv. Williams 82 seedlings germinated in vitro.


title: 199_xylem_rep1

description: Biological repetition 1 of genotype 199


title: 218_xylem_rep1

description: Biological repetition 1 of genotype 218


title: Rat_Lung_1wk_biological rep3


title: 214_xylem_rep1

description: Biological repetition 1 of genotype 214


title: 188_xylem_rep1

description: Biological repetition 1 of genotype 188


title: 195_xylem_rep1

description: Biological repetition 1 of genotype 195


title: 196_xylem_rep1

description: Biological repetition 1 of genotype 196


title: Rat_Kidney_1wk_biological rep2

description: Gene expression data from 1-wk-old rat kidney.

source_name: Kidney isolated from 1-wk-old rat


title: Rat_Kidney_1wk_biological rep5


title: 96_xylem_rep1

description: Biological repetition 1 of genotype 96


title: 200_xylem_rep1

description: Biological repetition 1 of genotype 200


title: yAPS3 - pool of anterior lobe prostate stroma laser capture microdissected from three young (4 month-old) mice

status: Public on Sep 15 2010

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

hyb_protocol: Experimental and reference probes were combined and competitively hybridized to MPEDB microarrays under a coverslip for 16 h at 63°C.

scan_protocol: Fluorescent array images were collected for Cy3 and Cy5 emissions using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA). Image intensity data were extracted and analyzed using GenePix 4.1 software.

data_processing: Spots of poor quality, as determined by visual inspection, were removed from further analysis. To normalize log-ratio data, a print-tip specific Lowess curve was fit to the log-intensity versus log-ratio plot, using 20.0% of the data to calculate the fit at each point. This curve was used to center the log-ratio for each spot. 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.

source_name: MGS

label_protocol: cDNA probe pairs were prepared by amino-allyl reverse transcription using 2 μg of amplified RNA and labeling with Cy3-dCTP or Cy5-dCTP fluorescent dyes (Amersham Bioscience, Piscataway, NJ.)

extract_protocol: Reference RNA was purified using Trizol (Life Technologies, Rockville, MD) following the manufacturer’s protocol. The RNA was then further purified by RNeasy maxi kit (Qiagen Inc, Valencia, CA) and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by one round of mRNA amplification using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

tag: gender

value: male

value: Swiss-Webster

value: Adult

value: reference pool of normal adult tissues (10% prostate and 30% each testis, liver, and kidney)

tag: amplification

value: one round aRNA

growth_protocol: Young (4 month-old) and old (20-24 monthold) C57BL/6 male mice were obtained from the National Institutes of Aging (NIA) Rodent Colony at Harlan Sprague Dawley (Chicago, IL) and maintained in a barrier facility and cared for in accordance with approved IACUC protocols. Following shipment, mice were acclimated to a common temperature, day-night cycle, and diet for at least 12 days to minimize environmental differences. Mice from each age group were randomized for the day and time of sacrifice. Following halothane anesthesia, mice were sacrificed by cervical dislocation. Prostates were rapidly excised, immersed in OCT embedding compound (Miles Diagnostics, Elkhart, Ind., USA) and snap-frozen in liquid nitrogen and stored at -80º C.

extract_protocol: Approximately 10,000 cells were laser-capture microdissected using the Veritas LCM system (Arcturus Mountain View, CA). Total RNA from LCM experimental samples were isolated using the Arcturus PicoPure RNA Isolation kit (Molecular Devices, Sunnyvale, CA) and DNAse-treated using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: 4 month-old

value: pool of anterior lobe prostate stroma laser capture microdissected from three mice

value: two round aRNA


title: Rat_Kidney_1wk_biological rep3

value: whole kidney

value: normal


title: Rat_Kidney_1wk_biological rep1

value: Sprague-Dawley


title: 92_xylem_rep1

description: Biological repetition 1 of genotype 92

value: xylem from field grown trees


title: yAPE3 - pool of anterior lobe prostate epithelium laser capture microdissected from three young (4 month-old) mice

value: pool of anterior lobe prostate epithelium laser capture microdissected from three mice


title: 101_xylem_rep1

description: Biological repetition 1 of genotype 101


title: 23_xylem_rep1

description: Biological repetition 1 of genotype 23


title: yDPS1 - pool of dorsal lobe prostate stroma laser capture microdissected from three young (4 month-old) mice

value: pool of dorsal lobe prostate stroma laser capture microdissected from three mice


title: oAPE1 - pool of anterior lobe prostate epithelium laser capture microdissected from three old (20-24 month-old) mice

value: 20-24 month-old


title: oAPE2 - pool of anterior lobe prostate epithelium laser capture microdissected from three old (20-24 month-old) mice


title: oAPS2 - pool of anterior lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice


title: yDPS2 - pool of dorsal lobe prostate stroma laser capture microdissected from three young (4 month-old) mice


title: yAPS1 - pool of anterior lobe prostate stroma laser capture microdissected from three young (4 month-old) mice


title: yAPS2 - pool of anterior lobe prostate stroma laser capture microdissected from three young (4 month-old) mice


title: 93_xylem_rep1

description: Biological repetition 1 of genotype 93


title: 110_xylem_rep1

description: Biological repetition 1 of genotype 110


title: yDPS3 - pool of dorsal lobe prostate stroma laser capture microdissected from three young (4 month-old) mice


title: P0_Ovary_CTGF_biological rep3

city: Pullman

first: Michael

middle: K

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

description: Gene expression data from rat P0 Ovary incubated in the presence of 500 ng/ml CTGF for 24 hours

hyb_protocol: Following fragmentation, ssDNA were hybridized  on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the   Affymetrix Fluidics Station 4500.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.

data_processing: The data were analyzed with Partek Genomic Suite 6.5 beta software  (Partek Inc., St. Louis, MO) using RMA, GC-content adjusted algorithm background correction, quintile normalization, median polish methods for probesets summarization, and log values of probes signals using base 2.  Organ culture date batch effect was removed.

label_protocol: Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).

growth_protocol: Zero-day old (< 8 hour old) female Sprague-Dawley rats (Harlan Laboratories, Inc., USA) were euthanized according to Washington State University IACUC approved protocols and the ovaries removed and cultured whole as described previously [Dole, G., et al., 2008].

extract_protocol: RNA was isolated from whole rat ovaries (2-3 ovaries per each sample) after homogenization in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.

treatment_protocol: For each ovary sample from which RNA was collected for microarrays, 1-3 ovaries per filter/well were cultured for 24 hours in the absence  (controls) or presence (treated) CTGF (human connective tissue growth factor)(500 ng/mL, PeproTech Inc., NJ USA).   Two or three ovaries from the same culture well (from different rat pups out of the same litter) and receiving the same treatment were pooled and homogenized together.

tag: organ culture date batch

value: Sprague-Dawley rat

value: Female

value: Rat ovary

tag: developmental stage

value: Rat ovary  at day P0 incubated for 24 more hours


title: yDPE1 - pool of dorsal lobe prostate epithelium laser capture microdissected from three young (4 month-old) mice

value: male

tag: strain

value: Swiss-Webster

value: Adult

value: pool of dorsal lobe prostate epithelium laser capture microdissected from three mice


title: oAPE3 - pool of anterior lobe prostate epithelium laser capture microdissected from three old (20-24 month-old) mice

value: reference pool of normal adult tissues (10% prostate and 30% each testis, liver, and kidney)

value: one round aRNA


title: oDPS1 - pool of dorsal lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice

value: two round aRNA


title: oDPS2 - pool of dorsal lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice


title: oDPS3 - pool of dorsal lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice


title: P0_Ovary_Control_biological rep3

description: Gene expression data from rat P0 Ovary incubated for 24 hours with no treatment


title: oAPS3 - pool of anterior lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice

value: pool of anterior lobe prostate stroma laser capture microdissected from three mice


title: oAPS1 - pool of anterior lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice


title: oDPE2 - pool of dorsal lobe prostate epithelium laser capture microdissected from three old (20-24 month-old) mice


title: P0_Ovary_CTGF_biological rep2

source_name: P0 Ovary incubated in the presence of 500 ng/ml CTGF for 24 hours


title: P0_Ovary_CTGF_biological rep1


title: oDPE3 - pool of dorsal lobe prostate epithelium laser capture microdissected from three old (20-24 month-old) mice


title: oDPE1 - pool of dorsal lobe prostate epithelium laser capture microdissected from three old (20-24 month-old) mice


title: P0_Ovary_Control_biological rep2

source_name: P0 Ovary incubated for 24 hours with no treatment


title: yAPE2 - pool of anterior lobe prostate epithelium laser capture microdissected from three young (4 month-old) mice

value: 4 month-old


title: yAPE1 - pool of anterior lobe prostate epithelium laser capture microdissected from three young (4 month-old) mice


title: Rat_Kidney_1wk_biological rep4

value: Sprague-Dawley

value: whole kidney

value: wild-type

value: 7 days old

value: normal


title: yDPE3 - pool of dorsal lobe prostate epithelium laser capture microdissected from three young (4 month-old) mice


title: P0_Ovary_Control_biological rep1

value: Sprague-Dawley rat

value: Female


title: yDPE2 - pool of dorsal lobe prostate epithelium laser capture microdissected from three young (4 month-old) mice


title: SA33591, biological rep3

city: Seoul

first: Taehoen

last: Lee

address: Gwanangno, Gwanak-gu

country: South Korea

institute: SNU

description: Gene expression data from overnight culture in tryptic soy broth

hyb_protocol: cRNA were hybridized for 16 hr at 45C on the GeneChip® S. aureus Genome arrays.

scan_protocol: GeneChip scanner 3000 (Affymetrix), controlled by GCOS Affymetrix software.

data_processing: The data were analyzed with RMA bioconductor, R packages.

organism: Staphylococcus aureus

source_name: Overnight culture of antibiotic resistant strain

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: We initiated S. aureus cultures at 37°C with shaking at 200 rpm using sterilized Tryptic Soy broth, after 24 hours, we diluted the cultures 1:100 in pre-warmed Tryptic Soy broth and incubated at 37°C with shaking at 200 rpm. Then, We harvested the cells by centrifugation at 3,000rpm for 30min.

extract_protocol: Total RNA was isolated according to TRIZOL protocol after cell disruption by lysis buffer and bead(J. Microbiological method 52:395-398)

tag: growth

value: Overnight culture

tag: antibiotics response

value: Resistant


title: SA33591, biological rep2


title: SA25923, biological rep1

source_name: Overnight culture of antibiotic sensitive strain

value: Sensitive


title: SA25923, biological rep2


title: SA25923, biological rep3


title: SA33591, biological rep1


title: Dif+LY d8B

city: Kansas City

first: Lindsey

middle: N

last: Kent

state: KS

address: 3901 Rainbow Blvd.

department: Pathology

institute: The University of Kansas Medical Center

description: Gene expression data from Differentiatied trophoblast stem cells treated with a PI3K inhibitor

hyb_protocol: RNA samples were hybridized to the Affymetrix 230 2.0 DNA microarray chip using the GeneChip® Hybridization Oven 640.  Washing and staining of hybridized chips were conducted using the GeneChip® Fluidics Station 450

scan_protocol: Chips were scanned using the Affymetrix GeneChip® Scanner 3000 with autoloader

data_processing: Hybridization signals were normalized with internal controls using the MAS5 algorithm in Affymetrix Expression Console.

source_name: Rcho-1 trophoblast stem cells differentiatied for 8 days in the precence of PI3K inhibitor LY294002 (10uM) for 8 days

label_protocol: Biotinylated

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

tag: cell type

tag: culture condition

value: NCTC 135 1% HS with 10uM LY294002

tag: cell line


title: Dif+LY d8C

value: Differentiatied trophoblast stem cells treated with a PI3K inhibitor


title: Dif+LY d8A


title: oDPSp3-2 - pool of dorsal lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice

hyb_protocol: Experimental and reference probes were combined and hybridized to custom Agilent 44K whole mouse genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2565BA (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software was used to normalize the Agilent array data using Agilent's default protocol (essentially LOWESS dye normalization on background subtracted signal values). Spots of poor quality or average intensity levels <300 were removed from further analysis.

label_protocol: A total of 825 ng of amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) following Agilent suggested protocols.

extract_protocol: Reference RNA was purified using Trizol (Life Technologies, Rockville, MD) following the manufacturer’s protocol. The RNA was then further purified by RNeasy maxi kit (Qiagen Inc, Valencia, CA) and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by one round of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: male

value: Swiss-Webster

value: Adult

tag: tissue

value: reference pool of normal adult tissues (10% prostate and 30% each testis, liver, and kidney)

extract_protocol: Approximately 10,000 cells were laser-capture microdissected using the Veritas LCM system (Arcturus Mountain View, CA). Total RNA from LCM experimental samples were isolated using the Arcturus PicoPure RNA Isolation kit (Molecular Devices, Sunnyvale, CA) and DNAse-treated using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl UTP incorporation into the second round aRNA using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: 20-24 month-old

value: pool of dorsal lobe prostate stroma laser capture microdissected from three mice


title: Dif d8C

description: Gene expression data from Differentiatied trophoblast stem cells

source_name: Rcho-1 trophoblast stem cells differentiatied for 8 days

value: Differentiatied trophoblast stem cells

value: NCTC 135 1% HS


title: 81_xylem_rep1

description: Biological repetition 1 of genotype 81

source_name: Eucalyptus grandis X Eucalyptus urophylla segregationg population; xylem tissue

value: xylem from field grown trees


title: 109_xylem_rep1

description: Biological repetition 1 of genotype 109


title: 76_xylem_rep1

description: Biological repetition 1 of genotype 76


title: oDPSp2-2 - pool of dorsal lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice

value: one round aRNA

value: two round aRNA


title: 114_xylem_rep1

description: Biological repetition 1 of genotype 114


title: oDPSp1b - pool of dorsal lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice


title: Dif d8B


title: Dif d8A


title: yDPSp2-2 - pool of dorsal lobe prostate stroma laser capture microdissected from three young (4 month-old) mice

value: 4 month-old


title: 88_xylem_rep1

description: Biological repetition 1 of genotype 88


title: Stem A

description: Gene expression data from Trophoblast stem cells

source_name: Rcho-1 trophoblast stem cells

value: Trophoblast stem cells

value: RPMI 1640 20%FBS


title: yDPSp1b - pool of dorsal lobe prostate stroma laser capture microdissected from three young (4 month-old) mice


title: yDPSp4 - pool of dorsal lobe prostate stroma laser capture microdissected from three young (4 month-old) mice


title: SMAD2 binding targets in murine R1 ES cells (2/2)

city: Beijing

first: Bing

last: Zhou

address: Datun Road

department: Center for Molecular Systems Biology

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565BA scanner and probe features were extracted using Feature Extraction Software (version 10.0)

data_processing: Log ratios were calculated by limma (Bioconductor package) and underwent Lowess normalization.

source_name: murine R1 ES cells, immuno-enriched DNA

label_protocol: DNA was labeled with CGH labeling kits (Invitrogen)

growth_protocol: Murine R1 ES cells were cultured under typical feeder free ES cell conditions (DMEM supplemented with Knockout serum replacement (Invitrogen Gibco), leukemia inhibitory factor (LIF), non-essential amino acids, GlutaMax-I (Invitrogen Gibco), β-mercaptoethanol and penicillin/streptomycin.

extract_protocol: R1 ES cells (5x107 – 1x108 cells) were chemically cross-linked by addition of one tenth volume of freshly-prepared 11% formaldehyde solution to cell media for 15 min at room temperature. Cells were rinsed twice with 1xPBS, harvested using a silicon scraper, frozen in liquid nitrogen and stored at -80°C prior to use. Cells were resuspended, lysed (1% SDS, 50 mM Tris pH 8.0, 5 mM EDTA, proteinase inhibitors), and sonicated to obtain DNA fragments of about 300-500bp length on average. Samples were then centrifuged at 14,000 rpm for 10 min. The supernatant was diluted (20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, proteinase inhibitors) and pre-absorbed by 50 ul protein A beads (Zymed) and then incubated with 10 ug antibodies (anti-Smad1/5) overnight at 4°C. The immunocomplex was collected with 100 ul protein A beads by 3 hour co-incubation and then washed sequentially with TSE I (0.1% SDS, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 150 mM NaCl, proteinase inhibitors), TSE II (0.1% SDS, 20 mM Tris pH 8.0, 2 mM EDTA, 1% Trion X-100, 500 mM NaCl, proteinase inhibitors), LiCl buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.25 mM LiCl, 0.1% NP-40, 1% deoxycholate sodium) and TE (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0). The bound immunocomplex was eluted with 400 ul fresh elution buffer (25 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) by heating at 65°C with occasional vortex for 15 min and crosslinking was reversed by overnight incubation at 65°C. Whole cell extract (WCE) DNA (Input fraction reserved from the sonication step) was also treated for crosslinking reversal. Immunoprecipitated DNA and WCE DNA were then purified by treatment with RNaseA, proteinase K and multiple phenol:chloroform:isoamyl alcohol extraction.

treatment_protocol: Undifferentiated ES cells under normal culture conditions

tag: sample type

value: Elute from a Smad2 chromatin immunoprecipitation

value: R1 ES cell

source_name: murine R1 ES cells, WCE DNA

value: Input for Smad2 chromatin immunoprecipitation


title: Stem B


title: oDPSp4b - pool of dorsal lobe prostate stroma laser capture microdissected from three old (20-24 month-old) mice

value: male


title: Ser7-phospho pol II, 25 deg

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

hyb_protocol: Hybridization was done by NimbleGen.

scan_protocol: Scanning was done by NimbleGen.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. The .gff files were provided by NimbleGen.

source_name: Ser7-PO4 4E12 monclonal ChIP DNA

label_protocol: Labelling was done by NimbleGen.

growth_protocol: Cells were grown in YPD to O.D. ~0.8.

extract_protocol: Cells were cross-linked in 1% formaldehyde 15 min 2 hr. and processed for ChIP as described in Schroeder et al. Genes Dev. 14:2435, 2000 (PMID 11018011). Rabbit anti-CTD antibody is described in Schroeder et al. 2000. Rabbit anti-Ser2-PO4 antibody is described in Zhang et al. EMBO J. 24:2379, 2005 (PMID 15944735). 4E12 monoclonal antibody is described in Chapman et al. Science 318:1780, 2007 (PMID 18079404). Rabbit anti-GFP antibody is from the Bentley lab (unpublished).

tag: background

tag: chip antibody

value: anti-Ser7-PO4 4E12 monoclonal

source_name: Input DNA

tag: antibody


title: yDPSp3-2 - pool of dorsal lobe prostate stroma laser capture microdissected from three young (4 month-old) mice

value: Swiss-Webster

tag: age

value: Adult


title: Ser2-phospho pol II, 23 deg

source_name: Ser2-PO4 polyclonal ChIP DNA

value: rabbit anti-Ser2-PO4


title: Total RNA pol II, pcf11-9 23 deg

source_name: Total RNA pol II ChIP DNA

treatment_protocol: Cells were synchronized in alpha factor followed by nocodozole (15 ug/ml) arrest for 1 hr 23 deg.

value: rabbit anti-pan CTD


title: Total RNA pol II, 37 deg

treatment_protocol: Cells were shifted from 25 to 37 deg for 2 hr.


title: Rat1

source_name: GFP-tagged Rat1 ChIP DNA

value: rabbit anti-GFP


title: Nrd1

source_name: myc-tagged Nrd1 ChIP DNA

value: mouse anti-myc 9E10 monoclonal

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody catalog #


title: Ser5-phospho pol II, 25 deg

source_name: Ser5-PO4 H14 monclonal ChIP DNA

value: mouse anti-Ser5-PO4 H14 monoclonal

value: Covance


title: Total RNA pol II, kin28as

treatment_protocol: Cells were treated with kinase inhibitor NP-PP1 (20 uM) 2 hr at 25 deg to inhibit Kin28.


title: Stem C


title: Pcf11

source_name: HA-tagged Pcf11 ChIP DNA

value: mouse anti-HA 12CA5 monoclonal

value: Roche


title: Total RNA pol II, pcf11-9 37 deg

treatment_protocol: Cells were synchronized in alpha factor followed by nocodozole (15 ug/ml) arrest for 1 hr 37 deg.


title: Nigriventris_female_repl6

city: Bloomington

first: Emilie

last: Snell-Rood

state: IN

address: 915 E 3rd St MY150

department: Biology

institute: Indiana University

description: This project sought to identify shared and divergent patterns of gene expression between two male morphs (horned/fighter and hornless/sneaker) of horned beetles in the genus Onthophagus.  We were interested in whether morph-biased expression was as divergent as sex-biased expression, so we also surveyed patterns of gene expression in females.  We investigated gene expression in three epidermal tissues (head horn, thoracic horn and legs) with respect to dorsal abdomindal epidermis, which does not express outgrowths.  We also surveyed gene expression in the central brain, relative to neural ganglia.

hyb_protocol: Labeled aRNAs from test and reference samples (adjusted to a total of 60pmol dye for each) were mixed with KREAblock (ULS aRNA Fluorescent Labeling kit, Kreatech, Amsterdam, Netherlands) and 2x enhanced cDNA hybridization buffer (Genisphere), and then heated at 80°C for 10 min. Microarrays were pre-treated for one hour at 55°C in pre-hybridization buffer consisting of 5xSSC, 0.1%SDS, and 1% I-block (Applied Biosystems, CA). Both mixed sample and the microarrays were kept at 55°C until hybridization. Hybridization was performed in a dark humidified chamber at 55°C overnight. Microarrays were rinsed in buffer A (2xSSC/0.2%SDS) at 55°C and then incubated in buffer A at 65°C for 10min. Arrays were then transferred to 2xSSC (room temperature) for 10 min, followed by incubation in 0.2x SSC for 10min (room temperature). Arrays were then dried by centrifugation at 500rcf for 4 min.

scan_protocol: Microarrays were scanned using a GenePix scanner 4200 (Molecular Devices).

data_processing: Data were filtered and extracted using GenePix v.5.0 and imported into Bioconductor. Normalization for M-values was performed using spatial and intensity dependent Lowess smoothing in OLIN and differential expression was assessed using Limma.

organism: Onthophagus nigriventris

source_name: Nigriventris female abdominal epidermis

label_protocol: RNA was amplified using a T7-based RNA amplification method (Klebes et al. 2002 (PMID 12186645)) as follows. One microgram of RNA was reverse transcribed using Oligo(dT)-T7 primer (Ambion) and SuperScriptIII reverse transcriptase (Invitrogen). Second strand synthesis was performed using DNA polymerase (Invitrogen) and RNase H (Invitrogen). In-vitro transcription was performed using the MEGAscript T7 kit (Ambion). Amplified RNA (aRNA) was labeled with Cy5 using the ULS aRNA Fluorescent Labeling Kit (Kreatech, Amsterdam, Netherlands).

growth_protocol: All animals were reared under controlled laboratory conditions.

extract_protocol: Total RNA was extracted from dissected tissue using Qiagen RNeasy kit according to the manufacturers protocol.

treatment_protocol: Wild type (unmanipulated) animals were used.

tag: species

value: Onthophagus nigriventris

tag: sex

value: female

tag: size

value: range

value: pupae within 24hrs after pupation

value: dissected dorsal abdominal epidermis

value: tissue pooled from 4 individuals

source_name: Nigriventris female thoracic epidermis

label_protocol: RNA was amplified using a T7-based RNA amplification method (Klebes et al. 2002 (PMID 12186645)) as follows. One microgram of RNA was reverse transcribed using Oligo(dT)-T7 primer (Ambion) and SuperScriptIII reverse transcriptase (Invitrogen). Second strand synthesis was performed using DNA polymerase (Invitrogen) and RNase H (Invitrogen). In-vitro transcription was performed using the MEGAscript T7 kit (Ambion). Amplified RNA (aRNA) was labeled with Cy3 using the ULS aRNA Fluorescent Labeling Kit (Kreatech, Amsterdam, Netherlands).

value: dissected dorsal prothoracic epidermis


title: Nigriventris_female_repl7

tag: developmental stage


title: Nigriventris_female_repl5


title: Nigriventris_female_repl3


title: Nigriventris_female_repl4


title: Total RNA pol II, ctk1-tet-degron

treatment_protocol: Cells were treated with doxycycline (10 ug/ml) at 37 deg 2 hr to deplete Ctk1.

tag: strain


title: Total RNA pol II, 23 deg


title: Nigriventris_large_male_repl5

source_name: Nigriventris large male thoracic epidermis

value: male

tag: morph

value: large, horned

source_name: Nigriventris large male abdominal epidermis


title: Nigriventris_female_repl2


title: Nigriventris_female_repl1


title: Nigriventris_large_male_repl4


title: Nigriventris_large_male_repl3


title: Nigriventris_large_male_repl2


title: Nigriventris_large_male_repl1


title: Nigriventris_small_male_repl7

source_name: Nigriventris small male thoracic epidermis

value: small, sneaker

source_name: Nigriventris small male abdominal epidermis


title: Nigriventris_small_male_repl6


title: IHA_245_1

city: Baltimore

first: Peter

last: Murakami

address: 855 N Wolfe St, Rangos 580

department: Center for Epigenetics

institute: Johns Hopkins University

description:
IHA_245_1 input
IHA_245_1 methyl-depleted

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in NimbleGen Hybridization solution master mix. Arrays were hybridized in Maui hybridization stations for 16-20 h at 42C, and washes were completed using manufacturer's protocols.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner per manufacturer's protocol.

data_processing:
Arrays were processed using Nimblescan 2.4 software. The data processing methods are described in Ayree, Z. Wu, C. Ladd-Acosta, B. Herb, A. Feinberg, S. Yegnasubramanian, R. Irizarry. Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics, (2010).
Briefly, processing involved background correction using a modified RMA convolution model, a modified control-probe loess procedure for within-array normalization, between-array normalization using quantile normalization, and estimation of percentages.

source_name: Input fraction from IHA_245_1

label_protocol: 2 µg of DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers for the input (UT) fraction and Cy5 nonamers for the methyl-depleted (MD) fraction per manufacturer's protocol.

extract_protocol: Genomic DNA (gDNA) were isolated using DNeasy kit (Qiagen) according to the manufacturer’s protocol. For each sample, 1~5 µg of genomic DNA was sheared into 1.6-3kb DNA size fragments, digested with the endonuclease McrBC, and fractionated on a 1% agarose gel alongside the sheared input (UT) fraction to enrich for the methyl-depleted (MD) fraction. The UT and MD fractions were purified and whole genome amplified using the WGA2 kit (Sigma) according to the manufacturer's protocol.

tag: cell type

value: lymphocyte

tag: bmi

tag: Sex

tag: timepoint

source_name: Methyl-depleted fraction from IHA_245_1


title: Nigriventris_small_male_repl5

tag: tissue

tag: sample type


title: IHA_247_1

description:
IHA_247_1 input
IHA_247_1 methyl-depleted

source_name: Input fraction from IHA_247_1

source_name: Methyl-depleted fraction from IHA_247_1


title: IHA_244_1

description:
IHA_244_1 input
IHA_244_1 methyl-depleted

source_name: Input fraction from IHA_244_1

source_name: Methyl-depleted fraction from IHA_244_1


title: Nigriventris_small_male_repl4


title: IHA_226_2

description:
IHA_226_2 input
IHA_226_2 methyl-depleted

source_name: Input fraction from IHA_226_2

source_name: Methyl-depleted fraction from IHA_226_2


title: Nigriventris_small_male_repl3


title: IHA_231_2

description:
IHA_231_2 input
IHA_231_2 methyl-depleted

source_name: Input fraction from IHA_231_2

source_name: Methyl-depleted fraction from IHA_231_2


title: IHA_231_1

description:
IHA_231_1 input
IHA_231_1 methyl-depleted

source_name: Input fraction from IHA_231_1

source_name: Methyl-depleted fraction from IHA_231_1


title: IHA_211_1

description:
IHA_211_1 input
IHA_211_1 methyl-depleted

source_name: Input fraction from IHA_211_1

source_name: Methyl-depleted fraction from IHA_211_1


title: IHA_244_2

description:
IHA_244_2 input
IHA_244_2 methyl-depleted

source_name: Input fraction from IHA_244_2

source_name: Methyl-depleted fraction from IHA_244_2


title: IHA_218_2

description:
IHA_218_2 input
IHA_218_2 methyl-depleted

source_name: Input fraction from IHA_218_2

source_name: Methyl-depleted fraction from IHA_218_2


title: IHA_247_2

description:
IHA_247_2 input
IHA_247_2 methyl-depleted

source_name: Input fraction from IHA_247_2

source_name: Methyl-depleted fraction from IHA_247_2


title: IHA_246_1

description:
IHA_246_1 input
IHA_246_1 methyl-depleted

source_name: Input fraction from IHA_246_1

source_name: Methyl-depleted fraction from IHA_246_1


title: IHA_226_1

description:
IHA_226_1 input
IHA_226_1 methyl-depleted

source_name: Input fraction from IHA_226_1

source_name: Methyl-depleted fraction from IHA_226_1


title: Nigriventris_small_male_repl2

source_name: Nigriventris small male thoracic epidermis

source_name: Nigriventris small male abdominal epidermis


title: IHA_196_2

description:
IHA_196_2 input
IHA_196_2 methyl-depleted

source_name: Input fraction from IHA_196_2

source_name: Methyl-depleted fraction from IHA_196_2


title: Direct_Head_epidermis_comparison_repl4

organism: Onthophagus taurus

source_name: Large male head epidermis

value: Onthophagus taurus

value: dissected dorsal head epidermis

source_name: Small male head epidermis


title: Nigriventris_small_male_repl1


title: IHA_246_2

description:
IHA_246_2 input
IHA_246_2 methyl-depleted

source_name: Input fraction from IHA_246_2

source_name: Methyl-depleted fraction from IHA_246_2


title: IHA_187_2

description:
IHA_187_2 input
IHA_187_2 methyl-depleted

source_name: Input fraction from IHA_187_2

source_name: Methyl-depleted fraction from IHA_187_2


title: Cellobiose grown cells vs Sucrose grown cells

city: Urbana

first: Carl

middle: James

last: Yeoman

state: IL

address: 1207 W Gregory ave

department: Institute for Genomic Biology

institute: University of Illinois

description: Biological replicate

hyb_protocol: 450ng in 10ul of each labelled cDNA (one labelled with Cy3, one with Cy5) was combined with 5ul of 10x Blocking agent (Agilent Technologies, Inc., Santa Clara, CA, USA), and this was combined with 25ul GEx Hybridization buffer HI-RPM (Agilent). The final solution was mixed with a pipettor, then 45ul was added to the array. The array was sealed within the hybridization chamber (Agilent Technologies, Inc.) and then incubated in an Hybridization oven (Agilent Technologies, Inc.) at 65 deg C for 16 hours. The hybridized arrays were subsequently transferred to a container of Wash solution 1 (Agilent Technologies, Inc.) and the coverslip was removed. The array was then washed firstly in a second volume of Wash solution 1 (Agilent Technologies, Inc.) and then in wash solution 2 (Agilent) prewarmed to 37 deg C, as per the manufacturers instructions. The slides were then dipped into a container of acetonitrile and finally rinsed in Stabilization and drying solution Agilent Technologies, Inc.) for 30 seconds. The slides were then removed and scanned immediately.

scan_protocol: Microarray slides were scanned at 5 uM using a GenePix professional 4200 scanner and GenePix 6.0 software (Molecular devices, Sunnyvale, CA). Scans were optimized using automated photo-multiplier tube (PMT) adjustment to give 0.02 % saturation.

data_processing: All resulting data was combined and analyzed using single channel analysis in bioconductor. Within array normalization was achieved using a background correction of half (anything below 0.5 is reset to 0.5).

organism: Xylanibacter ruminicola

source_name: Cellobiose grown cells

label_protocol: cDNAs were labelled using Cy3 and Cy5 dyes (GE healthcare, Piscataway, NJ, USA) as per the manufacturers instructions, All conditions had a minimum of three biological replicates including a dye-swap. Each gene was represented on the array by 5 identical 70mer probes for technical replication.

growth_protocol: P. ruminicola 23 (ATCC19189) was cultured anaerobically at 39 deg C in basal media containing 1.3 % (NH4)2SO4, 0.1% Hemin, 0.09% of each KH2PO4, NaCl and Methionine, 0.002% of each CaCl2 and MgCl2, 0.001% FeSO4, 0.0001% CoCl, 2.8x10^-2 M acetate, 9x10^-3 M propionate, 4.5x10^-3 n-butyrate, and 9x10^-4 of each isobutyrate, n-valerate, isovalerate and DL-2-methylbutyrate. The medium was supplemented with 30 mM (or an equivalent weight based upon the major constituent sugar for di-, tri-, oligo- and poly-saccharides) of the tested carbohydrate source. Cells were grown to mid-exponential growth phase as determined by OD at 600nm and then harvested by centrifugation.

extract_protocol: Harvested cells were ground under liquid nitrogen using an oven sterilized pestle and mortar. Cell homogenates were incubated in 1ml of Trizol (Invitrogen, Carlsbad, CA, USA) for 5 minutes at room temperature and then transferred to a sterile eppendorf tube. The homogenate was mixed with 200 ul of chloroform and the mixture was centrifuged at 12,000 x g for 15 mins at 4 deg C. The upper-acqueous layer was collected and RNA precipitated using 0.5 ml of isopropanol. Total RNA was pelleted by centrifgation at 12,000 x g for 20 mins at 4 deg C and then washed in 70 % ethanol (made up in DEPC-treated sterile ddH2O), before being resuspended in sterile DEPC-treated ddH2O. The resuspended DNA was then purified using an RNeasy kit (Qiagen, Hilden, Germany) as per the manufacturers instructions. Purified RNAs were analyzed for quality using a Bioanalyzer RNA 6000 nano-assay. All samples used gave an RNA index number (RIN) of 9 or greater. Total RNA was transcribed to cDNA using the Fairplay III system (Stratagene, La Jolla, CA)

treatment_protocol: The treatments were the different carbohydrate sources provided in the media for P. ruminicola to grow on. These were supplemented into the media prior to innoculation.

tag: growth conditions

value: Cellobiose grown

source_name: Sucrose grown cells

value: Sucrose grown


title: Xylose grown cells vs Sucrose grown cells

description: Biological replicate

source_name: xylose grown cells

value: xylose grown


title: Xylose grown cells vs Fructose grown cells

description: Biological replicate

source_name: Fructose grown cells

value: Fructose grown


title: IHA_187_1

description:
IHA_187_1 input
IHA_187_1 methyl-depleted

source_name: Input fraction from IHA_187_1

source_name: Methyl-depleted fraction from IHA_187_1


title: IHA_218_1

description:
IHA_218_1 input
IHA_218_1 methyl-depleted

source_name: Input fraction from IHA_218_1

source_name: Methyl-depleted fraction from IHA_218_1


title: Direct_Head_epidermis_comparison_repl2

description: This project sought to identify shared and divergent patterns of gene expression between two male morphs (horned/fighter and hornless/sneaker) of horned beetles in the genus Onthophagus.  We were interested in whether morph-biased expression was as divergent as sex-biased expression, so we also surveyed patterns of gene expression in females.  We investigated gene expression in three epidermal tissues (head horn, thoracic horn and legs) with respect to dorsal abdomindal epidermis, which does not express outgrowths.  We also surveyed gene expression in the central brain, relative to neural ganglia.


title: Soluble wheat arabinoxylan grown cells vs Arabinose grown cells

description: Biological replicate

source_name: Soluble wheat arabinoxylan

value: Soluble wheat arabinoxylan

source_name: Arabinose grown cells

value: Arabinose grown


title: IHA_207_2

description:
IHA_207_2 input
IHA_207_2 methyl-depleted

source_name: Input fraction from IHA_207_2

value: female

source_name: Methyl-depleted fraction from IHA_207_2


title: Switch grass grown cells vs Arabinose grown cells

description: Biological replicate

source_name: Switch grass grown cells

value: Switch grass grown


title: Direct_Head_epidermis_comparison_repl3

source_name: Small male head epidermis

value: pupae within 24hrs after pupation

source_name: Large male head epidermis


title: IHA_204_1

description:
IHA_204_1 input
IHA_204_1 methyl-depleted

source_name: Input fraction from IHA_204_1

source_name: Methyl-depleted fraction from IHA_204_1


title: IHA_191_1

description:
IHA_191_1 input
IHA_191_1 methyl-depleted

source_name: Input fraction from IHA_191_1

source_name: Methyl-depleted fraction from IHA_191_1


title: Direct_Head_epidermis_comparison_repl1

value: tissue pooled from 4 individuals


title: Sucrose grown cells vs Glucose grown cells

description: Biological replicate

source_name: Sucrose grown cells

source_name: Glucose grown cells

value: Glucose grown


title: IHA_190_2

description:
IHA_190_2 input
IHA_190_2 methyl-depleted

source_name: Input fraction from IHA_190_2

source_name: Methyl-depleted fraction from IHA_190_2


title: Small_male_thorax_repl4

source_name: Small male abdominal epidermis

value: male

value: dissected dorsal abdominal epidermis

source_name: Small male thoracic epidermis

value: dissected dorsal prothoracic epidermis


title: Switch grass grown cells vs Soluble wheat arabinoxylan grown cells

description: Biological replicate

source_name: Soluble wheat arabinoxylan


title: IHA_196_1

description:
IHA_196_1 input
IHA_196_1 methyl-depleted

source_name: Input fraction from IHA_196_1

value: lymphocyte

source_name: Methyl-depleted fraction from IHA_196_1


title: IHA_207_1

description:
IHA_207_1 input
IHA_207_1 methyl-depleted

source_name: Input fraction from IHA_207_1

source_name: Methyl-depleted fraction from IHA_207_1


title: IHA_186_2

description:
IHA_186_2 input
IHA_186_2 methyl-depleted

source_name: Input fraction from IHA_186_2

source_name: Methyl-depleted fraction from IHA_186_2


title: Starch grown cells vs Sucrose grown cells

description: Biological replicate

source_name: Starch grown cells

value: Starch grown


title: IHA_186_1

description:
IHA_186_1 input
IHA_186_1 methyl-depleted

source_name: Input fraction from IHA_186_1

source_name: Methyl-depleted fraction from IHA_186_1


title: Small_male_legs_repl4

source_name: Small male legs

value: Onthophagus taurus

value: small, sneaker

value: dissected legs


title: Small_male_head_repl4

source_name: Small male head epidermis

value: dissected dorsal head epidermis


title: Small_male_brain_repl4

source_name: Small male brain

value: dissected central brain and optic lobes

source_name: Small male ganglia

value: dissected subesophageal and thoracic ganglia


title: Starch grown cells vs Glucose grown cells

description: Biological replicate

source_name: Glucose grown cells


title: Small_male_legs_repl3

source_name: Small male abdominal epidermis


title: Raffinose grown cells vs Maltose grown cells

description: Biological replicate

source_name: Raffinose grown cells

value: Raffinose grown

source_name: Maltose grown cells

value: Maltose grown


title: Pullulan grown cells vs Arabinose grown cells

description: Biological replicate

source_name: Pullulan grown cells

value: Pullulan grown

source_name: Arabinose grown cells

value: Arabinose grown


title: Pullulan grown cells vs Cellibiose grown cells

description: Biological replicate

source_name: Cellobiose grown cells

value: Cellobiose grown


title: Small_male_head_repl3

value: pupae within 24hrs after pupation

value: tissue pooled from 4 individuals


title: Small_male_brain_repl3

value: male


title: IHA_180_2

description:
IHA_180_2 input
IHA_180_2 methyl-depleted

source_name: Input fraction from IHA_180_2

value: female

source_name: Methyl-depleted fraction from IHA_180_2


title: Small_male_thorax_repl2

source_name: Small male thoracic epidermis

value: dissected dorsal prothoracic epidermis

value: dissected dorsal abdominal epidermis


title: Small_male_thorax_repl3

value: Onthophagus taurus


title: Melibiose grown cells vs Galactose grown cells

description: Biological replicate

source_name: Melibiose grown cells

value: Melibiose grown

source_name: Galactose grown cells

value: Galactose grown


title: IHA_173_1

description:
IHA_173_1 input
IHA_173_1 methyl-depleted

source_name: Input fraction from IHA_173_1

value: lymphocyte

source_name: Methyl-depleted fraction from IHA_173_1


title: IHA_180_1

description:
IHA_180_1 input
IHA_180_1 methyl-depleted

source_name: Input fraction from IHA_180_1

source_name: Methyl-depleted fraction from IHA_180_1


title: IHA_176_2

description:
IHA_176_2 input
IHA_176_2 methyl-depleted

source_name: Input fraction from IHA_176_2

source_name: Methyl-depleted fraction from IHA_176_2


title: Melibiose grown cells vs Lactose grown cells

description: Biological replicate

source_name: Lactose grown cells

value: Lactose grown


title: Small_male_head_repl2

source_name: Small male head epidermis

value: small, sneaker

value: dissected dorsal head epidermis

source_name: Small male abdominal epidermis


title: Maltose grown cells vs Melibiose grown cells

description: Biological replicate

source_name: Maltose grown cells

value: Maltose grown


title: IHA_172_1

description:
IHA_172_1 input
IHA_172_1 methyl-depleted

source_name: Input fraction from IHA_172_1

source_name: Methyl-depleted fraction from IHA_172_1


title: IHA_172_2

description:
IHA_172_2 input
IHA_172_2 methyl-depleted

source_name: Input fraction from IHA_172_2

source_name: Methyl-depleted fraction from IHA_172_2


title: Small_male_brain_repl2

source_name: Small male ganglia

value: dissected subesophageal and thoracic ganglia

source_name: Small male brain

value: dissected central brain and optic lobes


title: Maltose grown cells vs Starch grown cells

description: Biological replicate

source_name: Starch grown cells

value: Starch grown


title: Mannose grown cells vs Pullulan grown cells

description: Biological replicate

source_name: Mannose grown cells

value: Mannose grown

source_name: Pullulan grown cells

value: Pullulan grown


title: Lactose grown cells vs Glucose grown cells

description: Biological replicate

source_name: Glucose grown cells

value: Glucose grown


title: Small_male_legs_repl2

source_name: Small male legs

value: male

value: pupae within 24hrs after pupation

value: dissected legs

value: tissue pooled from 4 individuals


title: Lactose grown cells vs Mannose grown cells

description: Biological replicate


title: Small_male_thorax_repl1

value: Onthophagus taurus

value: dissected dorsal abdominal epidermis

source_name: Small male thoracic epidermis

value: dissected dorsal prothoracic epidermis


title: Insoluble wheat arabinoxylan grown cells vs Switch grass grown cells

description: Biological replicate

value: Insoluble wheat arabinoxylan grown

source_name: Switch grass grown cells

value: Switch grass grown


title: Small_male_legs_repl1

value: small, sneaker


title: Glucose grown cells vs Xylose grown cells

description: Biological replicate

source_name: xylose grown cells

value: xylose grown


title: Small_male_head_repl1

source_name: Small male head epidermis

value: dissected dorsal head epidermis


title: Small_male_brain_repl1

value: dissected central brain and optic lobes

value: dissected subesophageal and thoracic ganglia


title: Large_male_thorax_repl4

source_name: Large male thoracic epidermis

value: large, horned

source_name: Large male abdominal epidermis


title: Galactose grown cells vs Raffinose grown cells

description: Biological replicate

source_name: Galactose grown cells

value: Galactose grown

source_name: Raffinose grown cells

value: Raffinose grown


title: IHA_168_1

description:
IHA_168_1 input
IHA_168_1 methyl-depleted

source_name: Input fraction from IHA_168_1

value: lymphocyte

value: female

source_name: Methyl-depleted fraction from IHA_168_1


title: Large_male_legs_repl4

source_name: Large male legs

value: male

value: pupae within 24hrs after pupation

value: dissected legs


title: IHA_165_2

description:
IHA_165_2 input
IHA_165_2 methyl-depleted

source_name: Input fraction from IHA_165_2

source_name: Methyl-depleted fraction from IHA_165_2


title: Glucose grown cells vs Maltose grown cells

description: Biological replicate

value: Glucose grown

source_name: Maltose grown cells

value: Maltose grown


title: Fructose grown cells vs Pullulan grown cells

description: Biological replicate

source_name: Fructose grown cells

value: Fructose grown

source_name: Pullulan grown cells

value: Pullulan grown


title: IHA_165_1

description:
IHA_165_1 input
IHA_165_1 methyl-depleted

source_name: Input fraction from IHA_165_1

source_name: Methyl-depleted fraction from IHA_165_1


title: Fructose grown cells vs Mannose grown cells

description: Biological replicate

source_name: Mannose grown cells

value: Mannose grown


title: Large_male_head_repl4

description: This project sought to identify shared and divergent patterns of gene expression between two male morphs (horned/fighter and hornless/sneaker) of horned beetles in the genus Onthophagus.  We were interested in whether morph-biased expression was as divergent as sex-biased expression, so we also surveyed patterns of gene expression in females.  We investigated gene expression in three epidermal tissues (head horn, thoracic horn and legs) with respect to dorsal abdomindal epidermis, which does not express outgrowths.  We also surveyed gene expression in the central brain, relative to neural ganglia.

value: Onthophagus taurus

value: dissected dorsal abdominal epidermis

value: tissue pooled from 4 individuals

source_name: Large male head epidermis

value: dissected dorsal head epidermis (head horn)


title: Galactose grown cells vs Mannose grown cells

description: Biological replicate


title: Large_male_thorax_repl3

value: large, horned

value: dissected dorsal prothoracic epidermis


title: Fructose grown cells vs Lactose grown cells

description: Biological replicate

source_name: Lactose grown cells

value: Lactose grown


title: Large_male_brain_repl4

source_name: Large male ganglia

value: dissected subesophageal and thoracic ganglia

source_name: Large male brain

value: dissected central brain and optic lobes


title: IHA_156_1

description:
IHA_156_1 input
IHA_156_1 methyl-depleted

source_name: Input fraction from IHA_156_1

value: lymphocyte

value: female

source_name: Methyl-depleted fraction from IHA_156_1


title: Cellobiose grown cells vs Xylose grown cells

description: Biological replicate

source_name: Cellobiose grown cells

value: Cellobiose grown

source_name: xylose grown cells

value: xylose grown


title: Large_male_legs_repl3

source_name: Large male abdominal epidermis

value: male

value: pupae within 24hrs after pupation

source_name: Large male legs

value: dissected legs


title: IHA_159_1

description:
IHA_159_1 input
IHA_159_1 methyl-depleted

source_name: Input fraction from IHA_159_1

source_name: Methyl-depleted fraction from IHA_159_1


title: IHA_152_1

description:
IHA_152_1 input
IHA_152_1 methyl-depleted

source_name: Input fraction from IHA_152_1

source_name: Methyl-depleted fraction from IHA_152_1


title: IHA_163_1

description:
IHA_163_1 input
IHA_163_1 methyl-depleted

source_name: Input fraction from IHA_163_1

source_name: Methyl-depleted fraction from IHA_163_1


title: IHA_152_2

description:
IHA_152_2 input
IHA_152_2 methyl-depleted

source_name: Input fraction from IHA_152_2

source_name: Methyl-depleted fraction from IHA_152_2


title: IHA_148_2

description:
IHA_148_2 input
IHA_148_2 methyl-depleted

source_name: Input fraction from IHA_148_2

source_name: Methyl-depleted fraction from IHA_148_2


title: Large_male_brain_repl3

source_name: Large male ganglia

source_name: Large male brain


title: Non-esterfied corn xylo-oligosaccharide grown cells vs Ester-enriched corn xylo-oligosaccharide grown cells

description: Biological replicate


title: Ester-enriched corn xylo-oligosaccharide grown cells vs Non-esterfied  corn xylo-oligosaccharide grown cells 1

description: Biological replicate


title: Large_male_thorax_repl2

source_name: Large male thoracic epidermis


title: IHA_154_1

description:
IHA_154_1 input
IHA_154_1 methyl-depleted

source_name: Input fraction from IHA_154_1

source_name: Methyl-depleted fraction from IHA_154_1


title: Arabinose grown cells vs insoluble Wheat arabinoxylan grown cells

description: Biological replicate

source_name: Arabinose grown cells

value: Arabinose grown

source_name: Insoluble wheat arabinoxylan grown cells

value: Insoluble wheat arabinoxylan grown