title: 1_cgpS_N_100_IPTG_csw

status: Public on Sep 14 2016

scan_protocol: After washing the microarrays were dried by centrifugation (5 min; 1,600 x g) and fluorescence was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) with 5 µm resolution using an Axon GenePix 4000B laser scanner (Axon Instruments, Sunnyvale, U.S.A).

data_processing: Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 7.0, Axon Instruments). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (www.bioconductor.org). Processed and normalized data as well as experimental details (according to MIAME) were stored in the in-house microarray database for further analysis. For determination of differentially expressed genes data were quality filtered as decribed (Polen et al., 2007) using Signal/Noise >=5 for Cy5 or Cy3 channel.

source_name: C. glutamicum empty plasmid

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described elsewhere (Polen T, Schluesener D, Poetsch A, Bott M, Wendisch VF (2007) Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol Lett. 273(1):109-19).

growth_protocol: The transcriptome of C. glutamicum, in which the CgpS protein was downregulated by countersilencing, was compared with the untreated transcriptome of C. glutamicum ATCC 13032 carrying the empty plasmid. Both strains were grown in defined minimal medium CGXII + 2 % glucose as sole carbon source and cultivated at 30°C. Cells were harvested at an OD600 of 5 in pre-cooled ice-filled tubes via centrifugation (4,500 x g, 10 min, and 4 °C) and subsequently frozen in liquid nitrogen as well as stored at -70°C until preparation of total RNA.

treatment_protocol: CGXII medium + 2 % glucose, 100 µM IPTG, 30°C

source_name: C. glutamicum pAN6 cgpS-N


title: Sample_2_Wt_vs_dpup_1uMFe_II

status: Public on Apr 04 2016

type: RNA

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

description: Sample 2

hyb_protocol: Purified cDNA samples to be compared were pooled and the prepared two-color samples were hybridized at 65°C while rotating for 17 hours using Agilent’s Gene Expression Hybridization Kit, hybridization oven and hybridization chamber. After hybridization the arrays were washed using Agilent’s Wash Buffer Kit according to the manufacturer’s instructions.

scan_protocol: Fluorescence of hybridized DNA microarrays was determined at 532 nm (Cy3) and 635 nm (Cy5) at 5 μm resolution with a GenePix 4000B laser scanner and GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA). Fluorescence images were saved to raw data files in TIFF format (GenePix Pro 6.0). Quantitative TIFF image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0).

data_processing: For calculation and normalization of ratios reflecting the relative mRNA levels (Ratio of Medians, GenePix Pro), GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

molecule: total RNA

organism: Corynebacterium glutamicum ATCC 13032

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm (2003) Appl. Environm. Microbiol. 69:2521-2532 and in Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott. (2004) Mol. Microbiol. 54: 420-438.

growth_protocol: DNA microarray analyses were performed to compare the mRNA levels of the C. glutamicum Δpup mutant and its parent wild type under iron-limited conditions. The two strains precultivated in CGXII medium with 4% (w/v) glucose and 1 µM FeSO4 were inoculated into fresh medium to an OD600 of 1, cultured for 2 h, and harvested on ice by centrifugation (5 min at 4,000 g and 4°C).

extract_protocol: The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004)  Mol Microbiol 54: 420-438.)

tag: genotype/variation

value: Δpup mutant

value: wild type


title: 2_cgpS_N_100_IPTG

organism: Corynebacterium glutamicum

extract_protocol: The preparation of total RNA was performed as described elsewhere with the RNeasy Kit from Qiagen (Polen T, Schluesener D, Poetsch A, Bott M, Wendisch VF (2007) Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol Lett. 273(1):109-19).

tag: growth phase

value: exponential


title: 3_cgpS_N_100_IPTG


title: Syn1Cre_Rep5_5; Syn1Cre_Rep6_10

status: Public on Mar 30 2020

type: SRA

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

country: USA

institute: Washington University

description:
SRT calling cards
Syn1Cre_Rep5_Ctx.ccf; Syn1Cre_Rep6_Ctx.ccf

library_source: transcriptomic

data_processing:
filtered for features of true insertion events (presence of piggyBac terminal repeat sequence; intact sequencing adapters, barcodes, and indexes; and a TTAA site)
mapped to build version mm10 of the mouse genome with Novoalign 3 (for SRT) or Bowtie2 (for BrokenHeart)
Reads aligning to the same TTAA with separate barcodes were considered unique insertions, and all analyses in this report considered all unique insertions equally, independent of read depth
Genome_build: mm10
Supplementary_files_format_and_content: .ccf files contain coordinates for each calling card insertion

organism: Mus musculus

source_name: Cortex

extract_protocol:
RNA was extracted from lysates with Qiagen RNeasy kit using manufacterer's protocols
SRT libraries were prepared from cortex RNA samples. Prior to library preparation, cortex samples were dissected into 10 separate pieces, from which RNA was independently isolated with the manufacturer’s protocol (Qiagen RNeasy kit, Germantown, MD, USA). This allows for identification of up to 10 independent insertion events into any TTAA site, given that these insertions occur in spatially separate samples. From these RNA samples, transposon sequencing libraries were generated with our bulk SRT protocol (Moudgil et al., in revision). In brief, RNA samples were first reverse transcribed, from which self-reporting transcripts, including flanking genomic sequences, were amplified via PCR. These amplicons were then tagged with universal Illumina sequencing overhangs, with separate indexes for libraries from each dissected piece, allowing for 10 ‘barcodes’ per sample and sequenced on Illumina HiSeq 2500 or NextSeq 500 platforms (Illumina, San Diego, CA, USA).
DNA was extracted from lysates with Qiagen DNeasy kit using manufacterer's protocols
BrokenHeart libraries were prepared from cortical DNA samples, as previously described (Wang et al., Genetics, 2012). A set of 20 individually barcoded BrokenHeart transposons were pooled and packaged into AAV. Thus, independent insertions into the same TTAA can be uniquely identified via barcode, removing the need to dissect and process tissue samples in separate pools as with SRT. Extracted DNA was self-ligated, amplified with inverse PCR, and sequenced with the Illumina NextSeq 500 platform (Illumina, San Diego, CA, USA).

treatment_protocol:
P0-1 AAV injection
P0-1 AAV injection

tag: 5' primer barcode

value: CGAAA; GTTAC


title: NK_4HBA_01

status: Public on Nov 28 2015

description: Sample 9

hyb_protocol: Custom-made whole-genome DNA microarrays for C. glutamicum ATCC 13032 printed with 70-mer oligonucleotides were obtained from Operon (Cologne, Germany) and are based on the genome sequence entry NC_006958. Hybridisation and stringent washing of the microarrays were performed according to the instructions of the supplier. Hybridisation was carried out for 16 - 18 h with Nexterion Oligo Hyb buffer (Shott, Jena, Germany) covered with a 25 mm x 60 mm LifterSlip (Implen, Munich, Germany) in a humid camber.

scan_protocol: After washing the microarrays were dried by centrifugation (5 min, 1600 g) and fluorescence was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) with 10 µm resolution using an Axon GenePix 4000B laser scanner (Axon Instruments, Sunnyvale, U.S.A).

source_name: C. glutamicum pulse

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Polen T, Schluesener D, Poetsch A, Bott M, Wendisch VF (2007) Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol Lett. 273(1):109-19.

growth_protocol: The transcriptome of C. glutamicum pulsed with 5 mM phenylpropanoid or 4-hydroxybenzoic acid was compared with the C. glutamicum ATCC13032, both grown in defined mineral medium CGXII + 4% glucose as sole carbon and energy source cultivated at 30°C. Cells were harvested at an OD600 of 5 in pre-cooled ice-filled tubes via centrifugation (4,500 x g, 10 min, and 4 °C) and subsequently frozen in liquid nitrogen as well as stored at -70°C until preparation of RNA. Transcriptome of deldetion strain C.g. deltacg0343 was compared to transcriptome of wt strain (same cultivation conditions as above).

treatment_protocol: CGXII medium 4 % glucose, 5 mM phenylpropanoid or 4-hydroxybenzoic acid (only for pulsing experiments), 30°C

tag: pulsed with

value: 5mM 4-hydroxybenzoic acid for 30min

source_name: C. glutamicum_control


title: MV_Zimt_01

description: Sample 13

value: 5mM cinnamic acid for 30min


title: NK_Cinnamat

description: Sample 8


title: NK_4HBA_02

description: Sample 10


title: NK_34HPP_01

description: Sample 11

value: 5mM 3-(4-hydroxyphenyl-)propionic acid for 30min


title: NK_Caffeat_02

description: Sample 2

value: 5mM caffeic acid for 30min


title: MV_Ferula_02

description: Sample 4

value: 5mM ferulic acid for 30min


title: NK_34HPP_02

description: Sample 12


title: MV_Zimt_02

description: Sample 14


title: HP1c

status: Public on May 01 2015

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description: genomic DNA

library_source: genomic

data_processing:
Basecalling was performed using CASAVA version 1.8
Quality control of FastQ sequences was assessed using the FastQC software version 0.9.3.
ChIP-seq reads were aligned to the dm3 genome assembly using Bowtie 0.12.5, rejecting reads aligning to more than one genomic location, allowing up to 2 mismatches in the first 28 bases of the reads and no gapped alignments.
Aligned reads were filtered with the htSeqTools R package. PCR artifacts were detected and removed with the filterDuplicateReads function using a FDR of 1%. Strand shift bias was removed using the alignPeaks function with the default options.
A first step for peak calling was done using the enrichedRegions function from the htSeqTools package to find genomic regions with coverage above 10 reads, comparing the proportion of reads inside/outside of each region between each IP sample and the Input with a logistic regression likelihood-ratio test. Enriched regions were defined as those with a Benjamini–Yekutieli adjusted P-value below 0.05.
In a second step, we used the function enrichedPeaks from htSeqTools to define peaks (i.e. putative binding sites) as locations within the enriched regions with a coverage difference between IP and Input above 30 reads for WOC/ROW/Z4 and 20 reads for HP1c/Dsk2.
After peak calling, we used the mergeRegions function from htSeqTools to merge adjacent peaks closer than 300bp.
Genome_build: dm3
Supplementary_files_format_and_content: BED files include chromosome, start and end of the identified peaks in the dm3 Drosophila melanogaster  genome.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were grown on Schneider’s insect Medium (Sigma) supplemented with 100 μg/ml streptomycin (Gibco), 100 units/ml penicilin (Gibco) and 10% FBS (Gibco)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with polyclonal αWOC, αROW, αZ4, αDsk2 and αHP1c antibodies. Finally DNA was purified by standard phenol extraction.
10 ng DNA, quantified by Qubit dsDNA HS Assay Kit (Invitrogen) was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 18 cycles was performed using TruSeqRNA Sample Prep Kit (Illumina) according to manufacturer’s recommendations. Purified libraries were quantified by Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution was evaluated using Bioanalyzer DNA 1000 assay (Agilent).

tag: type

value: IP

tag: cell line

value: S2 cells

tag: chip antibody

value: rabbit αHP1c


title: NK_wtCgCoumarPKS1

description: Sample 1

source_name: C. glutamicum + pulse

growth_protocol: The transcriptome of C. glutamicum pulsed with 5 mM p-coumaric acid was compared with the unpulsed C. glutamicum wt, both grown in defined mineral medium CGXII + 4% glucose as sole carbon and energy source cultivated at 30°C. Cells were harvested at an OD600 of 5 in pre-cooled ice-filled tubes via centrifugation (4,500 x g, 10 min, and 4 °C) and subsequently frozen in liquid nitrogen as well as stored at -70°C until preparation of RNA.

treatment_protocol: CGXII medium 4 % glucose, 5 mM p-coumaric acid, 30°C

value: 5 mM p-coumaric acid for 30min

source_name: C. glutamicum_unpulsed

value: none (unpulsed control)


title: NK_Coumarat

description: Sample 7

value: 5mM p-coumaric acid for 30min


title: MV_Cgdeltacg0343_02

description: Sample 6

source_name: C. glutamicum Δcg0343


title: Dsk2

description: genomic DNA

value: rabbit αDsk2


title: NK_wtCgCoumarPKS2

description: Sample 2


title: JVO1_vs_delta_fkpA_35degree_I

status: Public on Sep 08 2015

growth_protocol: The transcriptome of C. glutamicum JVO1 Delta-fkpA were compared with the reference C. glutamicum JVO1, both grown in defined mineral medium CGXII + 4% glucose as sole carbon and energy source cultivated at 35°C. Cells were harvested at an OD600 of 5 in pre-cooled ice-filled tubes via centrifugation (4,500 x g, 10 min, and 4 °C) and subsequently frozen in liquid nitrogen as well as stored at -70°C until preparation of RNA.

treatment_protocol: see growth protocol

tag: strain

tag: genotype

value: delta fkpA


title: JVO1_vs_delta_fkpA_35degree_II


title: NK_Caffeat_01

description: Sample 1

value: 5mM caffeic acid  for 30min


title: WT_with_MmC_vs_wo_MmC_3h_rep2

description: Sample 3

data_processing: For background correction of spot intensities, ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532 and in Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott. 2004. Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol. Microbiol. 54: 420-438.

growth_protocol: DNA microarrays; For transcriptome analysis C. glutamicum wild type cells were grown in 5 ml BHI (Brain Heart Infusion, Difco) for about 6 hours at 30°C. A second precultivation was performed in CGXII minimal medium containing 4% glucose as carbon source. From each preculture two main cultures were inoculated to an OD of 1 in CGXII minimal medium (4% glucose). At an OD of 3 Mitomycin C (final concentration of 0.6 µM) was added to one culture to induce the SOS response; the second, untreated culture served as reference. 5 ml samples were harvested by centrifugation (4000 x g, 10 min and 4 °C) at different time points after induction (one, three, and six hours). The cell pellet was subsequently frozen in liquid nitrogen and stored at -70°C until RNA preparation.

extract_protocol: The preparation of total RNA was performed as described previously with the RNeasy Kit from Qiagen (Möker, N., M. Brocker, S. Schaffer, R. Krämer, S. Morbach & M. Bott, (2004) Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol Microbiol 54: 420-438.)

value: wild type

tag: treated with

value: 0.6 mM mitomycin C for 3hr

value: none (untreated control) for 6hr


title: WT_with_MmC_vs_wo_MmC_3h_rep3

description: Sample 4

value: none (untreated control) for 3hr


title: MV_Cgdeltacg0343_01

description: Sample 5

value: exponential


title: MV_Ferula_01

description: Sample 3


title: WT_with_MmC_vs_wo_MmC_6h_rep3

description: Sample 6

value: 0.6 mM mitomycin C for 6hr


title: WT_with_MmC_vs_wo_MmC_6h_rep2

description: Sample 5


title: WT_with_MmC_vs_wo_MmC_1h_rep2

description: Sample 1

value: 0.6 mM mitomycin C for 1hr

value: none (untreated control) for 1hr


title: WT_with_MmC_vs_wo_MmC_1h_rep3

description: Sample 2


title: WT_with_MmC_vs_wo_MmC_6h

description: Sample 3


title: WT_with_MmC_vs_wo_MmC_3h

description: Sample 2


title: III_CgWT_Glu_MeOH_vs_CgWT_Glu

status: Public on Sep 27 2013

data_processing: Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 7.0, Axon Instruments). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (www.bioconductor.org).

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Frunzke, J., V. Engels, S. Hasenbein, C. Gätgens & M. Bott, (2008) Co-ordinated regulation of gluconate catabolism and glucose uptake in Corynebacterium glutamicum by two functionally equivalent transcriptional regulators, GntR1 and GntR2. Mol Microbiol 67: 305-322.

growth_protocol: Cells of a preculture in LB medium were used to inoculate a second preculture in CGXII minimal medium with 111 mM glucose. To test the influence of methanol in the presence of glucose, two parallel main cultures in CGXII minimal medium with 111 mM glucose were inoculated with the second preculture to an OD600 of 0.5. After reaching an OD600 of 5, 100 mM methanol was added to one culture whereas water was added to the second one as control. After continuing incubation for 30 minutes, cells of both cultures were harvested in pre-cooled (−20°C) ice-filled tubes via centrifugation (6,900 g, 10 min, 4 °C) and used for RNA isolation. To test the influence of methanol in absence of glucose, a preculture in CGXII medium with 111 mM glucose was incubated until an OD600 of 8 was reached. Cells were washed with CGXII minimal medium without a carbon source and resuspended in this medium to an OD600 of 5. The cell suspensions were incubated for 2 hours and then 100 mM methanol was added to one of the suspensions and water to the second one. After incubation for another 30 minutes, cells were harvested and used for RNA isolation.


title: II_CgWT_Glu_MeOH_vs_CgWT_Glu


title: I_CgWT_Glu_MeOH_vs_CgWT_Glu


title: CGXII_Delta_pup_vs_WT_II

status: Public on Jun 24 2014

growth_protocol: For growth in CGXII minimal media, a preculture 1 was grown in 5 ml BHI medium inoculated with a single colony from a fresh BHI agar plate and incubated at 170 rpm for 8 hours. Then 500 µl of preculture 1 were used to inoculate preculture 2 in 100 ml shake flasks with 20 ml CGXII minimal medium containing 4 % (w/v) glucose and incubated over night (140 rpm , 30 °C ). Subsequent main cultures (50 ml CGXII medium with 4 % glucose) were inoculated with cells from preculture 2 to an OD600 of about 0.4. For growth experiments in complex BHI medium, 20 ml brain heart infusion (BHI) medium (Difco Laboratories, Detroit, USA) were inoculated with a single colony from a fresh BHI agar plate and incubated at 140 rpm as overnight cultures. Subsequent main cultures (50 ml BHI medium) were inoculated with cells from overnight cultures to an optical density at 600 nm (OD600) of about 1. For DNA microarray  analysis, cells were harvested in the exponential growth phase at an OD600 of 4 to 5 by centrifugation with crushed ice (4°C; 4,000 x g; 3 min).

value: C. glutamicum delta pup

tag: sample

value: C. glutamicum type strain ATCC 13032


title: BHI_Delta_pup_vs_WT_I


title: CGXII_Delta_pup_vs_WT_III


title: Sample_1_BHI_Delta_pup_vs_WT_II_csw

growth_protocol: For growth experiments in complex BHI medium, 20 ml brain heart infusion (BHI) medium (Difco Laboratories, Detroit, USA) were inoculated with a single colony from a fresh BHI agar plate and incubated at 140 rpm as overnight cultures. Subsequent main cultures (50 ml BHI medium) were inoculated with cells from overnight cultures to an optical density at 600 nm (OD600) of about 1. For DNA microarray  analysis, cells were harvested in the exponential growth phase at an OD600 of 4 to 5 by centrifugation with crushed ice (4°C; 4,000 x g; 3 min).


title: II_CgWT_noC_vs_CgWT_noC_MeOH_csw


title: Delta-iolR_vs_WT_rep3

status: Public on Jul 29 2013

description: Sample 3

data_processing:
Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 7.0, Axon Instruments). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (www.bioconductor.org). Processed and normalized data as well as experimental details (according to MIAME) were stored in the in-house microarray database for further analysis.
lowess normalized log2 ration of (Delta-iolR/WT)  for spots having Signal/Noise >10 in channel 1 or channel 2, otherweise signals were considered as too low and disregarded

source_name: Delta-iolR

growth_protocol: The transcriptome of the deletion mutant ΔiolR was compared with the C. glutamicum wild type using whole-genome based DNA microarrays. For this purpose the strains were inoculated from a 5 ml BHI with 2% (wt/vol) glucose preculture into a second preculture in 50 ml CGXII minimal medium with 4% (wt/vol) glucose. For main culture, cells were cultivated in 50 ml CGXII minimal medium with 4% (wt/vol) glucose and harvested at an OD600 of about 5 in pre-cooled ice-filled tubes via centrifugation (6900 x g, 10 min, and 4 °C). The cell pellet was subsequently frozen in liquid nitrogen and stored at -70°C until RNA preparation.

value: Delta-iolR

value: early exponential (OD600 of about 5)

source_name: WT

tag: tag


title: I_CgWT_noC_MeOH_vs_CgWT_noC


title: WT_vs_Δcg2910_ExpC

status: Public on Jan 13 2014

data_processing: For ratio calculation and ratio normalization, GPR-files were processed using the BioConductor R-packages limma and marray (http://www.bioconductor.org).

source_name: ATCC 13032 CGXII glucose

growth_protocol: For transcriptome analysis C. glutamicum wild type and Δcg2910 cells were grown in 5 ml BHI (Brain Heart Infusion, Difco) for about 6 hours at 30°C. A second precultivation was performed in CGXII minimal medium containing 2% (w/v) glucose as carbon source. The main cultures were inoculated to an OD of 0.5 in CGXII minimal medium with 2% (w/v) glucose. At an OD of 5 the cells were harvested by centrifugation (4120 x g, 10 min and 4 °C). The cell pellet was subsequently frozen in liquid nitrogen and stored at -70°C.

source_name: 13032 Δcg2910 CGXII glucose

value: cg2910 deletion mutant


title: WT_vs_Delta-iolR_rep2

description: Sample 2


title: WT_vs_Δcg2910_ExpB


title: WT_with_MmC_vs_wo_MmC_1h

description: Sample 1


title: Sample_2_BHI_Delta_pup_vs_WT_III


title: WT_vs_Δcg2910_ExpA


title: CGXII_Delta_pup_vs_WT_I

growth_protocol: For growth in CGXII minimal media, a preculture 1 was grown in 5 ml BHI medium inoculated with a single colony from a fresh BHI agar plate and incubated at 170 rpm for 8 hours. Then 500 µl of preculture 1 were used to inoculate preculture 2 in 100 ml shake flasks with 20 ml CGXII minimal medium containing 4 % (w/v) glucose and incubated over night (140 rpm , 30 °C ). Subsequent main cultures (50 ml CGXII medium with 4 % glucose) were inoculated with cells from preculture 2 to an OD600 of about 0.4. For DNA microarray  analysis, cells were harvested in the exponential growth phase at an OD600 of 4 to 5 by centrifugation with crushed ice (4°C; 4,000 x g; 3 min)


title: 9000137, rep2

status: Public on Mar 22 2013

city: Boston

first: Katrina

last: Steiling

state: MA

address: 72 East Concord Street, E-631

department: Medicine

institute: Boston Univeristy School of Medicine

description:
AS_SL_E4_137rehyb
High MW RNA.
Gene expression data from bronchial brushing.

hyb_protocol: The labeled fragmented cDNA was hybridized to Affymetrix Human Gene ST v1.0 microarrays for 16-18 hours in the GeneChip Hybridization Oven 640 (45C, 60rpm rotation). The hybridized samples were washed. Using Affymetrix Fluidics Station 450 (Hybridization Washing and Staining Kit, Affymetrix), the samples were first stained with streptavidin (SAPE). This was followed by signal amplification with a biotinylated goat anti-streptavidin antibody and a second SAPE stain.

scan_protocol: Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix).

data_processing: RMA, EntrezGene v11.0.1 CDF.

label: biotin

organism: Homo sapiens

source_name: bronchial brushing

label_protocol: High molecular weight RNA was processed and hybridized to Affymetrix Human Gene Arrays ST v1.0 as described in the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix). Briefly, 200ng of high molecular weight RNA was reverse transcribed (Whole Transcript cDNA Synthesis Kit, Affymetrix). The resulting cDNA was used as a template for in vitro transcription (IVT) (Whole Transcript cDNA Amplification Kit, Affymetrix). The resulting antisense cRNA was purified (GeneChip Sample Cleanup Module, Affymetrix) and then reverse transcribed with dUTP incorporation (Whole Transcript cDNA Synthesis Kit, Affymetrix, Santa Clara, CA). The resulting single-stranded sense DNA was fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1). The fragmented DNA was labeled using DNA Labeling Reagent which is covalently linked to biotin with terminal deoxynucleotidyl transferase (TdT) (Whole Transcript Terminal Labeling Kit, Affymetrix).

extract_protocol: Isolation of high molecular weight RNA was performed using the miRNeasy mini kit (Qiagen) as per the manufacturer's instructions. Briefly, bronchial epithelial cells were lysed and homogenized in QIAzol Lysis Reagent. After chloroform extraction, the aqueous phase containing RNA was mixed with ethanol. This was applied to an RNeasy Mini Spin Column to retain high molecular weight RNA (>200 nt). After washing, high molecular weight RNA was eluted.

tag: patient number

tag: used in analysis

value: no

tag: copd

tag: age (years)

tag: smoking status

tag: Sex

tag: pack years

tag: history of asthma

tag: inhaled medications

tag: tissue

value: bronchial epithelial cells

tag: change in fev1


title: 9000093

description:
AS_SL93
High MW RNA.
Gene expression data from bronchial brushing.


title: 9000121

description:
AS_SL_D4_121
High MW RNA.
Gene expression data from bronchial brushing.


title: 9000137

description:
AS_SL_E4_137
High MW RNA.
Gene expression data from bronchial brushing.


title: 9000149, rep2

description:
AS_SL_E5_149rehyb
High MW RNA.
Gene expression data from bronchial brushing.


title: 8000544

description:
AS_SL_C2_544
High MW RNA.
Gene expression data from bronchial brushing.


title: 9000301

description:
AS_SL301
High MW RNA.
Gene expression data from bronchial brushing.


title: 5000691

description:
AS_COPD_B_A3_5000691
High MW RNA.
Gene expression data from bronchial brushing.


title: Delta-iolR_vs_WT_rep1

description: Sample 1

tag: genotype/variation

tag: growth phase


title: 9000149

description:
AS_SL_E5_149
High MW RNA.
Gene expression data from bronchial brushing.


title: 6000189

description:
AS_COPD_D1_6000189
High MW RNA.
Gene expression data from bronchial brushing.


title: 6000399

description:
AS_COPD_A3_6000399
High MW RNA.
Gene expression data from bronchial brushing.


title: 5000548

description:
AS_COPD_B6_5000548
High MW RNA.
Gene expression data from bronchial brushing.


title: 4000605

description:
AS_COPD_B_B6_4000605
High MW RNA.
Gene expression data from bronchial brushing.


title: 4000250

description:
AS_COPD_A5_4000250
High MW RNA.
Gene expression data from bronchial brushing.


title: 5000114

description:
AS_COPD_D3_5000114
High MW RNA.
Gene expression data from bronchial brushing.


title: 4000514

description:
AS_COPD_A6_4000514
High MW RNA.
Gene expression data from bronchial brushing.


title: 4000071

description:
AS_COPD_E6_4000071
High MW RNA.
Gene expression data from bronchial brushing.


title: 1272

description:
AS_COPD_A4_1272
High MW RNA.
Gene expression data from bronchial brushing.


title: 1886

description:
AS_COPD_D5_1886
High MW RNA.
Gene expression data from bronchial brushing.


title: 1774

description:
AS_COPD_A_A8_1774
High MW RNA.
Gene expression data from bronchial brushing.


title: 4000240

description:
AS_COPD_A_C6_4000240
High MW RNA.
Gene expression data from bronchial brushing.


title: 4000081

description:
AS_COPD_E5_4000081
High MW RNA.
Gene expression data from bronchial brushing.


title: 4000222

description:
AS_COPD_B5_4000222
High MW RNA.
Gene expression data from bronchial brushing.


title: 1666

description:
AS_COPD_B1_1666
High MW RNA.
Gene expression data from bronchial brushing.


title: 5000249

description:
AS_COPD_D4_5000249
High MW RNA.
Gene expression data from bronchial brushing.


title: 1554

description:
AS_COPD_F4_1554
High MW RNA.
Gene expression data from bronchial brushing.


title: 1058

description:
AS_COPD_A1_1058
High MW RNA.
Gene expression data from bronchial brushing.


title: 891

description:
AS_COPD_A_A4_891
High MW RNA.
Gene expression data from bronchial brushing.


title: 1729

description:
AS_COPD_A2_1729
High MW RNA.
Gene expression data from bronchial brushing.

value: yes


title: 4000395

description:
AS_COPD_D2_4000395
High MW RNA.
Gene expression data from bronchial brushing.


title: 1141

description:
AS_COPD_B_A1_1141
High MW RNA.
Gene expression data from bronchial brushing.


title: WT_vs_Delta-chrSA_Heme_rep3

status: Public on Oct 31 2012

data_processing: Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 7.0, Axon Instruments). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (www.bioconductor.org). Processed and normalized data as well as experimental details (according to MIAME) were stored in the in-house microarray database for further analysis.

growth_protocol: The transcriptome of the deletion mutant ΔchrSA grown on heme or FeSO4 were compared with the C. glutamicum wild type using whole-genome based DNA microarrays. For this purpose the strains were inoculated from a 5 ml BHI preculture into a second preculture in 50 ml CGXII medium containing 1 µM FeSO4. For main culture, cells were cultivated in 50 ml CGXII minimal medium with 4% glucose (w/v) containing either 2.5 µM FeSO4 or 2.5 µM hemin as iron source and harvested at an OD600 of 5 to 6 in pre-cooled ice-filled tubes via centrifugation (6900 x g, 10 min, and 4 °C). The cell pellet was subsequently frozen in liquid nitrogen and stored at -70°C until RNA preparation.

tag: iron source

value: hemin

value: deletion mutant ΔchrSA


title: Delta-chrSA_vs_WT_Heme_rep2

value: wild type


title: Delta-chrSA_vs_WT_Fe_rep1


title: Delta-chrSA_vs_WT_Fe_rep2


title: Delta-chrSA_vs_WT_Heme_rep1


title: 21.25 µM copper: wildtype_vs_Delta copRS rep5

status: Public on Sep 05 2011

hyb_protocol: Custom-made whole-genome DNA microarrays for C. glutamicum ATCC 13032 printed with 70-mer oligonucleotides were obtained from Operon (Cologne, Germany) and are based on the genome sequence entry NC_006958. Hybridisation and stringent washing of the microarrays were performed according to the instructions of the supplier. Hybridisation was carried out for 16 - 18 h at 42°C using a MAUI hybridization system (BioMicro Systems, Salt Lake City, USA).

scan_protocol: After washing the microarrays were dried by centrifugation (5 min, 1600 g) and fluorescence was determined at 532 nm (Cy3-dUTP) and 635 nm (Cy5-dUTP) with 10 µm resolution using an Axon GenePix 6000 laser scanner (Axon Instruments, Sunnyvale, U.S.A).

data_processing: Quantitative image analysis was carried out using GenePix image analysis software and results were saved as GPR-file (GenePix Pro 6.0, Axon Instruments). For data normalization, GPR-files were processed using the BioConductor/R-packages limma and marray (www.bioconductor.org). Processed and normalized data as well as experimental details (according to MIAME) were stored in the in-house microarray database for further analysis.

source_name: wt; 21.25 µM copper

label_protocol: Synthesis of fluorescently labelled cDNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532

growth_protocol: Bacterial strains, media and growth conditions. For growth experiments or DNA microarray analysis 5 ml of brain heart infusion (BHI) medium (Difco Laboratories, Detroit, MI) were inoculated with colonies from a fresh BHIS agar plate (BHI agar with 0.5 M sorbitol) and incubated for 6 hours at 30°C and 170 rpm. This first preculture was used to inoculate a 500-ml shake flask containing 50 ml CGXII minimal medium (19) with 4% (w/v) glucose added as carbon source with 1.25 µM or 21.25 µM CuSO4. The second preculture was cultivated overnight at 30°C and then used to inoculate the main culture to an optical density at 600 nm (OD600) of ~1 in a 500-ml shake flask containing 50 ml CGXII minimal medium (19) with 4% (w/v) glucose with 1.25 µM or 21.25 µM CuSO4. For DNA microarray analysis cells were harvested at an OD600 of 5-6.

extract_protocol: Preparation of total RNA were carried out as described in Lange, C., D. Rittmann, V. F. Wendisch, M. Bott, and H. Sahm. 2003. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl. Environm. Microbiol. 69:2521-2532

tag: treatment

value: 21.25 uM copper

tag: genotype

source_name: DcopRS; 21.25 µM copper

value: 21.25 µM copper

value: Delta copRS


title: WT_vs_Delta-chrSA_Fe_rep3

value: exponential


title: wildtype: 21.25 µM copper_vs_1.25 µM copper rep3

source_name: wt; 1.25 µM copper

value: 1.25 µM copper


title: wildtype: 21.25 µM copper_vs_1.25 µM copper rep2


title: wildtype: 21.25 µM copper_vs_1.25 µM copper rep4


title: 21.25 µM copper: wildtype_vs_Delta copRS rep3


title: 21.25 µM copper: wildtype_vs_Delta copRS rep4


title: wildtype: 21.25 µM copper_vs_1.25 µM copper rep1


title: 21.25 µM copper: wildtype_vs_Delta copRS rep1


title: 21.25 µM copper: wildtype_vs_Delta copRS rep2


title: WT_vs_DhrrA_FeSO4 1

status: Public on Dec 17 2010

growth_protocol: Bacterial strains, media and growth conditions. For growth experiments or DNA microarray analysis 5 ml of brain heart infusion (BHI) medium (Difco Laboratories, Detroit, MI) were inoculated with colonies from a fresh BHIS agar plate (BHI agar with 0.5 M sorbitol) and incubated for 6 hours at 30°C and 170 rpm. This first preculture was used to inoculate a 500-ml shake flask containing 50 ml CGXII minimal medium (19) with 4% (w/v) glucose added as carbon source and 1 uM FeSO4. The second preculture was cultivated overnight at 30°C and then used to inoculate the main culture to an optical density at 600 nm (OD600) of ~1. The trace element solution as well as the iron source (in the main culture either 0.5 uM FeSO4, 0.5 uM hemin were added after autoclaving. A 1 mM hemin stock solution was prepared in 100 mM KOH and stored at 4°C. For DNA microarray analysis cells were harvested at an OD600 of 5-6.

value: wildtype

source_name: DhrrA

value: DhrrA


title: WT_vs_DhrrA_FeSO4 3


title: wildtype: FeSO4_vs_heme 1

source_name: heme

value: heme


title: wildtype: FeSO4_vs_heme 2


title: WT_vs_DhrrA_heme 3


title: Glutamine_vs_Ammonia_rep1

status: Public on Oct 05 2010

source_name: Glutamine

growth_protocol: Bacterial strains, media and growth conditions. The C. glutamicum type strain ATCC 13032 was used as wild type. For growth experiments and DNA microarray experiments, cells from a fresh LB agar plate were inoculated into 70 ml  LB medium in a 500 ml baffled shake flask and this first preculture was incubated at 30°C and 120 rpm. For DNA microarray experiments, cells were washed in culture medium without any carbon and nitrogen source and the second preculture and subsequently the main culture were inoculated to an optical density at 600 nm (OD600) of 0.1 and 0.5, respectively, in 60 ml CgXII minimal medium without urea and ammonium sulphate, which contained 0.03 g/l 3,4-dihydroxybenzoate and 0.2 mg/l biotin. For growth experiments the main culture was inoculated to an OD600 of 0.5 to 1. The medium contained 70 mM glucose as carbon and energy source. As sole nitrogen source either 150 mM ammonium sulphate or 70 mM glutamine were used.

tag: strain

value: type strain ATCC 13032

source_name: Ammonia


title: WT_vs_DhrrA_heme 1


title: wildtype: FeSO4_vs_heme 3


title: Ammonia_vs_Glutamine_rep2

description: Ammonia_vs_Glutamine_rep2, dye swap


title: WT_vs_DhrrA_heme 2


title: 96 day human retina

city: Seattle

first: Thomas

last: Reh

state: WA

address: 815 Mercer St

department: Biological Structure

institute: University of Washington

description: 96 day human retina

hyb_protocol: Following fragmentation, cRNA were hybridized on Human Gene 1.0 ST array, washed and stained as per manufacturer guidelines.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Affymetrix® Expression Console™ Software.

source_name: Cells from human fetal retina age 96 days

label_protocol: Cy3 cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Retinas were either directly used or maintained in culture with IRBP-GFP lentivirus for 4 days till GFP was observed

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

tag: cell type

value: retinal cells


title: Human Healthy Retina 1

status: Public on Oct 14 2010

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Human Healthy Retina 1

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the 7G scanner in Sankara Nethralaya.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data was analyzed using GeneSpring GX v 10.0.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended Quantile normalization
Summarization Algorithm: ExonRMA16
Transcript level: CORE
Technology: Affymetrix.HuGene-1_0-st-v1
Normalization: Quantile
Baseline Transformation: median of all samples

source_name: Retina from healthy adult

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: No growth conditions

extract_protocol: RNA was isolated from 1mg of Retinoblastoma tumors with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. The extracted RNA was quantified using nanodrop and the purity was analysed by Agilant Bioanalyser with RNA nano chip and the RNAs with RIN values of 6 and above were considered for further processing.

treatment_protocol: chemotherapy of one sample (139-09) is 10 cycles and other sample (984-09) is 8 cycles.

value: cadeveric eye

value: primary cultured cells


title: Human Healthy Retina 2

description: Human Healthy Retina 2


title: WT_vs_DhrrA_FeSO4 2