characteristic: ENA-FIRST-PUBLIC

text: CRI

text: public

text: ArrayExpress

text: Norway rat

text: Protocols: Step1 RNA extraction 1. Excise 25 mg liver tissue sample (on dry ice) into Precellys tubes CK28-R, bertin technology 2. Remove the sample tube from the dry ice and immediately pipet 700 ul QIAzol Lysis Reagent into each sample tube. 3. Homogenize immediately on the TissueLyser for 2x10 5000 with 10 break 4. Place the sample tube containing the homogenate on the benchtop at room temperature (15-25C) for 5 min. This step promotes dissociation of nucleoprotein complexes. 5. Add 140 ul chloroform and shake it vigorously for 15s. Thorough mixing is important for subsequent phase separation. 6. Place the sample tube on the benchtop at room temperature for 2-3 min. 7. Centrifuge at >6000 x g (max. 9000 x g for Precellys tubes) for 15 min at 4C. After centrifugation, the sample separates into 3 phases: an upper, colorless, aqueous phase containing RNA; a white interphase enriched with DNA; and a lower, red, organic phase containing proteins. For tissues with an especially high fat content, an additional, clear phase may be visible below the red, organic phase. The volume of the aqueous phase should be approximately 350 ul. 8. Transfer the upper aqueous phase to a new reaction tube. Centrifuge again if a little bit of the red organic phase was transferred accidentally. This is important because it will interfere with the downstream precipitation. 9. Add 1 Vol% of isopropanol and mix thoroughly. Incubate 15 min at RT 10. Centrifuge full-speed, 20 min, 4C. 11. Wash with 750 ul 75% EtOH 12. Centrifuge full-speed, 10 min, 4C 13. Allow pellet to air-dry 14. Dissolve pellet in 20-50 ul RNase-free water Step2 , Turbo Dnase treat (Ambion AM1907) 10ug Total RNA, 1/10th volume DNase buffer (10ul), Turbo DNase enzyme (2ul), Water (to 100ul) Incubate 37C 30 minutes (mix inactivation agent) 0.15 volume inactivation agent (15ul) Step4, Ribominus treat (Invitrogen K1550-02) Hybridization Step Instructions are provided below to perform hybridization for 1-10ug of your total RNA sample with the RiboMinus(tm) Eukaryote Probe. To process >10 ug total RNA sample, divide your sample into two samples, each containing <10 ug total RNA. 1. Set a water bath or heat block to 70-75C. 2. To a sterile, RNase-free 1.5 mL microcentrifuge tube, add the following: Total RNA (1-10 ug): <10 uL, RiboMinus(tm) Probe (15 pmol/uL): 10uL, Hybridization Buffer: 100 uL. 3. Incubate the tube at 70-75C for 5 minutes to denature RNA. 4. Allow the sample to cool to 37C slowly over a period of 30 minutes by placing the tube in a 37C water bath. To promote sequence-specific hybridization, it is important to allow slow cooling. Do not cool samples quickly by placing tubes in cold water. 5. While the sample is cooling down, proceed to Preparing Beads. 1. Resuspend RiboMinus(tm) Magnetic Beads in its bottle by thorough vortexing. 2. Pipet 750 uL of the bead suspension into a sterile, RNase-free, 1.5 mL microcentrifuge tube. 3. Place the tube with the bead suspension on a magnetic separator for 1 minute. The beads settle to the tube side that faces the magnet. Gently aspirate and discard the supernatant. 4. Add 750 uL sterile, DEPC Water to the beads and resuspend beads by slow vortexing. 5. Place tube on a magnetic separator for 1 minute. Aspirate and discard the supernatant. 6. Repeat Steps 4-5 once. 7. Resuspend beads in 750 uL Hybridization Buffer and transfer 250 uL beads to a new tube and maintain the tube at 37C for use at a later step. 8. Place the tube with 500 uL beads on a magnetic separator for 1 minute. Aspirate and discard the supernatant. 9. Resuspend beads in 200 uL Hybridization Buffer and keep the beads at 37C until use. Removing rRNA 1. After the incubation at 37C for 30 minutes of the hybridized sample (above), briefly centrifuge the tube to collect the sample to the bottom of the tube. 2. Transfer the sample (~120 uL) to the prepared RiboMinus(tm) Magnetic beads from Step 9 (Preparing Beads, above). Mix well by pipetting up and down or low speed vortexing. 3. Incubate the tube at 37C for 15 minutes. During incubation, gently mix the contents occasionally. Briefly centrifuge the tube to collect the sample to the bottom of the tube. 4. Place the tube on a magnetic separator for 1 minute to pellet the rRNA-probe complex. Do not discard the supernatant. The supernatant contains RiboMinus(tm) RNA. 5. Place the tube with 250 uL beads from Step 7 (Preparing Beads, above) on a magnetic separator for 1 minute. Aspirate and discard the supernatant. 6. To this tube of beads, add ~320 uL supernatant containing RiboMinus(tm) RNA from Step 4, above. Mix well by pipetting up and down or low speed vortexing. 7. Incubate the tube at 37C for 15 minutes. During incubation, gently mix the contents occasionally. Briefly centrifuge the tube to collect the sample to the bottom of the tube. 8. Place the tube on a magnetic separator for 1 minute to pellet the rRNA-probe complex. Do not discard the supernatant as the supernatant contains RiboMinus(tm) RNA. Concentrating RiboMinus(tm) RNA Using Ethanol Precipitation To ensure recovery of smaller (<200 nt) RNA, concentrate the RiboMinus(tm) RNA using ethanol precipitation as described below or using a modified RiboMinus(tm) Concentration Module (Cat. no. K1550-05) protocol with 60% ethanol (protocol included with the kit). 1. Transfer the RiboMinus(tm) RNA sample into a clean, RNAse-free 1.5 mL or 2 mL microcentrifuge tube. 2. Add the following components to RiboMinus(tm) RNA: - 1 mL glycogen (20 mg/mL) - 1/10th sample (eluted RNA) volume (30 uL for this protocol) of 3 M sodium acetate - 2.5X sample volumes (750 uL for this protocol) of 100% ethanol . Step First Strand cDNA synthesis ( Invitrogen 11917-010 ). mRNA 10ul, oligo dT 1ul, random primer 1ul, Incubate 70C 5 minutes then transfer to ICE for a few minutes. 5x FSS buffer 5ul, DTT2.5ul, dNTP1ul, RNase out 1ul, Water 2.5ul. Incubate 25C for 2 minutes then:1ul Superscript 2 42C 1 hour ( minimal ) Or 1ul Superscript 3 46C 1 hour ( minimal )70C 15 minutes to inactivate. Use Qiagen PCR column to remove dNTP from FSS reaction. Elute 50ul water or EB. Step 4 Second Strand Synthesis Make up 10mM DUTP mix ( Promega U1335 )(dATP, dCTP, dGTP, dUTP) Make up reaction on ice Volume cDNA from step 3 50ul 5x FSS buffer, 4ul DTT 2ul, 5xSSS buffer 30ul DU/NTP mix 3ul, E.coli DNA ligase 1ul, E.Coli DNA polymerase 3ul, E.Coli Rnase H1ul, Water 56ul, Incubate 16C for 2 hours, Add 2ul T4 DNA polymerase 5 minutes 16C. Qiagen column purification column Elute 50ul water or EB. Nanodrop sample ( in my experience i had around 500ng cDNA ). Take 250ng (store any remainder -20C) and make up to 300ul with water ( arbitrary amount ). Step 5 Sonication Bioruptor 2 x 5minutes 30 sec ON 30 sec OFF, full power changing ice in between. Ethanol PPT. Prepare cDNA for sequencing by attaching adapters as per Illumina manufacturesrs instructions, exept for modification, before PCR amplification treat sample with 1ul Uracil N-glycosylase (UNG) 37C 15minutes ( Applied Biosystems ).

text: adult

text: Rattus norvegicus

characteristic: organism

text: Rattus norvegicus

text: liver

text: Rattus norvegicus

text: male


status: PUBLIC

tag: attribute

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CRI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Norway rat

characteristic: common name

text: Protocols: Samples were prepared by direct perfusion of the tissue with buffered salt solution, followed by % formaldehyde. After 10 minutes, the tissue was removed and diced in 500 mM glycine buffer to neutralize the formaldehyde. After homogenization, the cells were rinsed with PBS. The animal tissues were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from an mass equivalent of 1/4 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA - version 2.2) with the following modifications. The ChIP-enriched DNA was not further fragmented. After end-repair and addition of an A base to the 3prime ends, the adapters were ligated to the ends of the DNA Fragments using 2 ul of fortyfold diluted 'Adapter oligo mix' in a total reaction volume of 25 ul. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 ul of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to the manufacturer's protocols, with single-end sequencing for 36 to 45 cycles.

characteristic: description

text: adult

characteristic: developmental stage

text: Rattus norvegicus

text: Rattus norvegicus

text: liver

characteristic: organism part

text: Rattus norvegicus

text: male

characteristic: sex

characteristic: title

type: has member


characteristic: ENA-FIRST-PUBLIC

text: CRI

text: public

text: ArrayExpress

text: southeastern Asian house mouse

text: adult

text: Mus Castaneus

text: Mus musculus castaneus

text: liver

text: Mus musculus castaneus

text: male


text: CRI

text: public

characteristic: StrainOrLine

text: ArrayExpress

text: house mouse

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CRI

text: public

text: ArrayExpress

text: southeastern Asian house mouse

text: adult

text: Mus Castaneus

text: Mus musculus castaneus

text: liver

text: Mus musculus castaneus

text: male


text: CRI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male


E-MTAB-861:Central starchy endosperm 2

text: GATC Biotech AG

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-861:Central starchy endosperm 2

tag: Namespace:GATC Biotech AG

text: 14 d

characteristic: age

text: ArrayExpress

text: bread wheat

text: Protocols: Heads were tagged at anthesis and pure starchy endosperm dissected at 10, 14, 17, 21, and 28dpa for transcript analysis. The outside two florets on the central four spikelets on each side of the ear, in total 16 caryopses, were dissected to yield pure central starchy endosperm of the developing grain. Each head was considered a biological replicate for the qRT analysis, and up to 10 replicates were pooled for the RNA sequencing and biochemical analysis. Dissected samples were immediately frozen in liquid nitrogen, lyophilised, and homogenised in a TissueLizer (Qiagen). Bread wheat (Triticum aestivum) cv Cadenza plants were grown in controlled environment as described in Sparks and Jones, 2009, (In HD Jones, PR Shewry, eds, Transgenic Wheat, Barley and Oats. Humana Press, pp 71-92).

text: anthesis

characteristic: initial time point

text: Triticum aestivum

text: Triticum aestivum

text: starchy endosperm

text: Triticum aestivum

text: Central starchy endosperm 2


E-MTAB-861:Central starchy endosperm 1

text: GATC Biotech AG

text: public

characteristic: SRA accession

text: E-MTAB-861:Central starchy endosperm 1

characteristic: Submitter Id

text: 10 d

text: ArrayExpress

characteristic: broker name

text: bread wheat

characteristic: common name

text: anthesis

text: Triticum aestivum

text: Triticum aestivum

text: starchy endosperm

text: Triticum aestivum

text: Central starchy endosperm 1


E-MTAB-861:Central starchy endosperm 3

text: GATC Biotech AG

text: public

text: E-MTAB-861:Central starchy endosperm 3

text: 17 d

text: ArrayExpress

text: bread wheat

characteristic: description

text: anthesis

text: Triticum aestivum

text: Triticum aestivum

text: starchy endosperm

characteristic: organism part

text: Triticum aestivum

text: Central starchy endosperm 3


E-MTAB-861:Central starchy endosperm 5

characteristic: ENA-FIRST-PUBLIC

text: GATC Biotech AG

text: public

text: E-MTAB-861:Central starchy endosperm 5

text: 28 d

text: ArrayExpress

text: bread wheat

text: anthesis

text: Triticum aestivum

text: Triticum aestivum

text: starchy endosperm

text: Triticum aestivum

text: Central starchy endosperm 5

characteristic: title


E-MTAB-861:Central starchy endosperm 4

text: GATC Biotech AG

text: public

text: E-MTAB-861:Central starchy endosperm 4

text: 21 d

text: ArrayExpress

text: bread wheat

text: anthesis

text: Triticum aestivum

characteristic: organism

text: Triticum aestivum

text: starchy endosperm

text: Triticum aestivum

text: Central starchy endosperm 4


text: Tbr iSeq

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Trypanosome_iSeq_profiling-sc-2011-12-05T11:47:39Z-991248

text: Trypanosoma brucei

text: RNAi induced genomic T brucei DNA samples grown in Pentamidine for 7-10 days

characteristic: sample description

text: Trypanosoma brucei


text: Tbr iSeq

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Trypanosome_iSeq_profiling-sc-2011-12-05T11:47:23Z-991247

text: Trypanosoma brucei

text: RNAi induced genomic T brucei DNA samples grown in Nifurtimox for 7-10 days

text: Trypanosoma brucei


text: Tbr iSeq

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Trypanosome_iSeq_profiling-sc-2011-12-05T11:46:40Z-991245

text: Trypanosoma brucei

text: RNAi induced genomic T brucei DNA samples grown in Eflornithine for 7-10 days

text: Trypanosoma brucei


text: Tbr iSeq

text: SC

text: public

characteristic: SRA accession

text: Trypanosome_iSeq_profiling-sc-2011-12-05T11:47:08Z-991246

text: Trypanosoma brucei

text: RNAi induced genomic T brucei DNA samples grown in Melarsoprol for 7-10 days

text: Trypanosoma brucei


text: Tbr iSeq

text: SC

text: public

text: Trypanosome_iSeq_profiling-sc-2011-12-05T11:47:56Z-991249

characteristic: Submitter Id

text: Trypanosoma brucei

text: RNAi induced genomic T brucei DNA samples grown in Suramin for 7-10 days

text: Trypanosoma brucei


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: GMISNU

text: public

text: human

text: Transcriptome sequencing of liver metastatic lung adenocarcinoma of AK55

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

characteristic: common name

text: exome sequencing from microgram amounts of tumour material

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: exome sequencing from nanogram amounts of matched normal material

characteristic: description

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: exome sequencing from microgram amounts of matched normal material

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: exome sequencing from nanogram amounts of tumour material

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: exome sequencing from microgram amounts of HapMap sample

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: public

text: human

text: exome sequencing from nanogram amounts of HapMap sample

text: Homo sapiens

text: Homo sapiens


text: OICR

text: public

text: human

text: iPS derived from fibroblasts

text: Homo sapiens

text: Homo sapiens


text: SRA-Webin

text: GMISNU

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: Liver metastatic lung cancer sample used for whole-genome sequncing


GFP 5 Day

text: SRA-Webin

text: DPSQ

text: public

text: GFP 5 Day

text: Schmidtea

text: Schmidtea

text: asexual clonal line 5 day after GFP RNAi


Wildtype control

text: SRA-Webin

text: DPSQ

text: public

text: Wildtype control

text: Schmidtea

text: Schmidtea

text: wildtype control for irradiation


H2B 5 Day

text: SRA-Webin

text: DPSQ

text: public

text: H2B 5 Day

text: Schmidtea

text: Schmidtea

text: asexual clonal line 5 day after H2B RNAi


H2B 2 Day

text: SRA-Webin

text: DPSQ

text: public

text: H2B 2 Day

text: Schmidtea

text: Schmidtea

text: asexual clonal line 2 day after H2B RNAi


Irradiation 2 Days

text: SRA-Webin

text: DPSQ

text: public

text: Irradiation 2 Days

text: Schmidtea

text: Schmidtea

text: asexual clonal line 2 day after irradiation


H2B 1 Day

text: SRA-Webin

text: DPSQ

text: public

text: H2B 1 Day

text: Schmidtea

text: Schmidtea

text: asexual clonal line 1 day after H2B RNAi


Irradiation 4 Days

text: SRA-Webin

text: DPSQ

text: public

text: Irradiation 4 Days

text: Schmidtea

text: Schmidtea

text: asexual clonal line 4 day after irradiation


text: public

tag: Namespace:Michael Smith Genome Sciences Centre, Vancouver, Canada

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: Megakaryoblastic Leukemia

characteristic: cell type

text: human

text: Protocols: CHRF 288-11 cells were cultured in RPMI-1640 (Sigma-Aldrich, Gillingham, UK, R0883), 10 % FBS (Invitrogen, Paisley, UK, 10100-147) and 200 uM L-glutamine, 100 U penicillin and 100 ug/ml streptomycin (Sigma-Aldrich, G1146). 20 million CHRF cells per condition were crosslinked for 10 minutes with 1% formaldehyde. Cells were lysed for 10 minutes on ice (10 mM Tris pH8.0, 10 mM NaCl, 0.2% NP-40, Complete). Nuclei were lysed with for 10 minutes on ice (50 mM Tris pH8.1, 10 mM EDTA, 1% SDS, Complete). Crosslinked chromatin was sheared for 2x5 minutes by sonication using a Bioruptor (Diagenode, Cambridge, UK) and pre-cleared with 100 ug anti-rabbit IgG pre-immune serum (Sigma-Aldrich I5006) using protein G sepharose beads (Roche Diagnostics, Burgess Hill, UK, 11 243 233 001). Chromatin immunoprecipitation was performed over night in IP dilution buffer (20 mM Tris pH8.1, 2mM EDTA, 150 mM NaCl, 1% Triton X100, 0.01% SDS), using 14 ug anti-Meis1 (Abcam, Cambridge, UK, ab19867, Lot No. 153899). Beads were washed twice with wash buffer 1 (20 mM Tris pH 8.1, 2 mM EDTA, 50 mM NaCl, 1 % Triton X100, 0.1 % SDS), once with wash buffer 2 (10 mM Tris pH 8.1, 1 mM EDTA, 250 mM LiCl, 1% NP40, 1% sodium deoxycholate monohydrate) and twice with TE buffer. Bound chromatin was eluted from the beads twice with 100 mM NaHCO3, 1 % SDS. After reverse-crosslinking, RNaseA and proteinase K digestion, chromatin was cleaned up using the Qiagen PCR purification kit (Qiagen, Crawley, UK, 28104).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: CHRF


characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: ArrayExpress

text: human

text: Protocols: CHRF 288-11 cells were cultured in RPMI-1640 (Sigma-Aldrich, Gillingham, UK, R0883), 10 % FBS (Invitrogen, Paisley, UK, 10100-147) and 200 uM L-glutamine, 100 U penicillin and 100 ug/ml streptomycin (Sigma-Aldrich, G1146). We performed FAIRE in the human megakaryocytic cell line CHRF-288-11. Cells were maintained in RPMI-1640 medium (Sigma-Aldrich, R0883), 20 % horse serum (heat- inactivated, Invitrogen, 26050-088), and 1 % L-glutamine-penicillin-streptomycin solution (Sigma-Aldrich, G1146), and grown at 37C, 5 % CO2, and 100% humidified atmosphere. FAIRE experiments were carried out as previously described. Twenty million cells were cross-linked with 1 % formaldehyde for 12 min and subjected to 12 sonication cycles (30 sec of high pulse, 30 sec of rest) using the Bioruptor UCD-200. A DNA amplification step was neglected. The sample was cleaned-up using the QIAGEN MinElute PCR Purification Kit (Qiagen, 28004). FAIRE DNA was processed following the Illumina paired-end library generation protocol.

text: megakaryoblastic leukaemia

characteristic: disease state

text: CHRF

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: CHRF

characteristic: title


characteristic: ENA-LAST-UPDATE

text: SRA-Webin

characteristic: External Id

text: UU

characteristic: INSDC center name

text: public

text: dog

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Ancient DNA isolated from a prehistoric domestic dog from Linköping, Sweden


text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: megakaryocyte

text: human

text: Protocols: MKs were obtained by culture of CD34+ hematopoietic progenitor cells. In short, cord blood was collected with informed consent and CD34+ cells were prepared by magnetic bead selection. Purified cells were cultured (1x105 cells/ml) for 10 days in serum-free medium supplemented with human thrombopoietin and interleukin-1beta to differentiate into MKs.By day 10 more than 90% of cells stained positive for CD41 positive and negative for CD34. Total RNA was obtained by the Trizol method. Polyadenylated RNA was purified from this by two rounds of magnetic Oligo dT25 selection (Dynabeads Oligo (dT)25, Invitrogen) in the presence of RNase inhibitor (New England Biolabs, Hitchin, UK), combined with DNase treatment (DNA-free, Ambion, Invitrogen). The mRNA was fragmented using RNA fragmentation reagent (Ambion, Invitrogen) and precipitated with added glycogen (Ambion, Invitrogen), then cDNA produced by Superscript Double Stranded cDNA synthesis kit (Invitrogen), replacing oligo-dT primer with random primer. Thereafter, library preparation was as per mRNA-sequencing kit (Illumina, Little Chesterford, UK), starting with end repair.

text: Homo sapiens

text: Homo sapiens

text: cord blood

characteristic: organism part

text: Homo sapiens


text: GSC:MIxS v2.1

characteristic: ENA-CHECKLIST

text: GSC, MIxS

characteristic: ENA-KEYWORD

text: Germany, Lower Saxony

text: VTI

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: BBCH 63 - 65; August 2009

characteristic: collection date

text: maize culticar Benicia

characteristic: current vegetation

text: 2-15 cm

unit: m

characteristic: depth

text: Rhizosphere microbial communities were extracted by saline washes of fine roots (diameter > mm) of maize cultivar Benicia, collected at the flowering stage BBCH 63-65. Individual plants were sampled. Total DNA was extracted from the collected cells by “FastDNA SPIN kit for soil” (MP Biomedicals, Illkirch, France). The extraction included two bead beating steps of 45 s at 6.5 m s-1 on a FastPrep-24 system (MP Biomedicals) and additional washing steps of the binding matrix each with 1 ml 5.5 M guanidine thiocyanate (Carl Roth GmbH) until the matrix retained its original color (1 - 3 washes).

text: soil

characteristic: enviornmental package

text: field soil; ENVO:00005755

characteristic: environment (featurel)

text: rhizosphere; ENVO:00005801

characteristic: environment (material)

text: 52° N

characteristic: geographic location (latitude)

text: 10° E

characteristic: geographic location (longitude)

text: MIMARKS

characteristic: investigation type

characteristic: nucleic acid extraction

text: rhizosphere metagenome

text: initial denaturation: 95degC_15min; 30 cycles of: denaturation: 94degC_60s, annealing: 50degC_60s, extention: 72degC_70s; final extension at 72degC_5min

characteristic: pcr conditions

text: F_Com1_MID2: ccatctcatccctgcgtgtctccgactcagACGCTCGACACAGCAGCCGCGGTAATAC; R_Com2: cctatcccctgtgtgccttggcagtctcagCCGTCAATTCCTTTGAGTTT

characteristic: pcr primers

characteristic: ph

text: maize rhizosphere

characteristic: project name

text: rhizosphere metagenome

text: Pyrosequencing

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene


text: GSC:MIxS v2.1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: GSC, MIxS

characteristic: ENA-KEYWORD

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Germany, Lower Saxony

text: VTI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: BBCH 63 - 65; August 2009

text: maize culticar 3BT

text: 2-15 cm

text: Rhizosphere microbial communities were collected by saline washes of fine roots (diameter > mm) of maize cultivar 3BT, collected at the flowering stage BBCH 63-65. Individual plants were sampled. Total DNA was extracted from the collected cells by “FastDNA SPIN kit for soil” (MP Biomedicals, Illkirch, France). The extraction included two bead beating steps of 45 s at 6.5 m s-1 on a FastPrep-24 system (MP Biomedicals) and additional washing steps of the binding matrix each with 1 ml 5.5 M guanidine thiocyanate (Carl Roth GmbH) until the matrix retained its original color (1 - 3 washes).

characteristic: description

text: soil

text: field soil; ENVO:00005755

text: rhizosphere; ENVO:00005801

text: 52° N

text: 10° E

text: MIMARKS

text: rhizosphere metagenome

characteristic: organism

text: F_Com1_MID9: ccatctcatccctgcgtgtctccgactcagTAGTATCAGCCAGCAGCCGCGGTAATAC; R_Com2: cctatcccctgtgtgccttggcagtctcagCCGTCAATTCCTTTGAGTTT

text: maize rhizosphere

text: rhizosphere metagenome

text: Pyrosequencing

text: 16S rRNA

characteristic: title


text: GSC:MIxS v2.1

text: GSC, MIxS

text: Germany, Lower Saxony

text: VTI

text: public

text: BBCH 63 - 65; August 2009

characteristic: collection date

text: maize culticar DKC 4250

characteristic: current vegetation

text: 2-15 cm

characteristic: depth

text: Rhizosphere microbial communities were extracted by saline washes of fine roots (diameter > mm) of maize cultivar DKC 4250, collected at the flowering stage BBCH 63-65. Individual plants were sampled. Total DNA was extracted from the collected cells by “FastDNA SPIN kit for soil” (MP Biomedicals, Illkirch, France). The extraction included two bead beating steps of 45 s at 6.5 m s-1 on a FastPrep-24 system (MP Biomedicals) and additional washing steps of the binding matrix each with 1 ml 5.5 M guanidine thiocyanate (Carl Roth GmbH) until the matrix retained its original color (1 - 3 washes).

text: soil

characteristic: enviornmental package

text: field soil; ENVO:00005755

characteristic: environment (featurel)

text: rhizosphere; ENVO:00005801

characteristic: environment (material)

text: 52° N

characteristic: geographic location (latitude)

text: 10° E

characteristic: geographic location (longitude)

text: MIMARKS

characteristic: investigation type

characteristic: nucleic acid extraction

text: rhizosphere metagenome

characteristic: pcr conditions

text: F_Com1_MID4: ccatctcatccctgcgtgtctccgactcagAGCACTGTAGCAGCAGCCGCGGTAATAC; R_Com2: cctatcccctgtgtgccttggcagtctcagCCGTCAATTCCTTTGAGTTT

characteristic: pcr primers

characteristic: ph

text: maize rhizosphere

characteristic: project name

text: rhizosphere metagenome

text: Pyrosequencing

text: 16S rRNA


text: GSC:MIxS v2.1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: GSC, MIxS

characteristic: ENA-KEYWORD

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Germany, Lower Saxony

text: VTI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: BBCH 63 - 65; August 2009

text: maize culticar DKC 5143

text: 2-15 cm

text: Rhizosphere microbial communities were collected by saline washes of fine roots (diameter > mm) of maize cultivar DKC 5143, collected at the flowering stage BBCH 63-65. Individual plants were sampled. Total DNA was extracted from the collected cells by “FastDNA SPIN kit for soil” (MP Biomedicals, Illkirch, France). The extraction included two bead beating steps of 45 s at 6.5 m s-1 on a FastPrep-24 system (MP Biomedicals) and additional washing steps of the binding matrix each with 1 ml 5.5 M guanidine thiocyanate (Carl Roth GmbH) until the matrix retained its original color (1 - 3 washes).

characteristic: description

text: soil

text: field soil; ENVO:00005755

text: rhizosphere; ENVO:00005801

text: 52° N

text: 10° E

text: MIMARKS

text: rhizosphere metagenome

text: F_Com1_MID6: ccatctcatccctgcgtgtctccgactcagATATCGCGAGCAGCAGCCGCGGTAATAC; R_Com2: cctatcccctgtgtgccttggcagtctcagCCGTCAATTCCTTTGAGTTT

text: maize rhizosphere

text: rhizosphere metagenome

text: Pyrosequencing

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene


text: GSC:MIxS v2.1

text: GSC, MIxS

text: Germany, Lower Saxony

text: VTI

text: public

text: BBCH 63 - 65; August 2009

characteristic: collection date

text: maize culticar 3BT

characteristic: current vegetation

text: 2-15 cm

characteristic: depth

text: Rhizosphere microbial communities were collected by saline washes of coarse roots (diameter 2-4 mm) of maize cultivar 3BT, collected at the flowering stage BBCH 63-65. Individual plants were sampled. Total DNA was extracted from the collected cells by “FastDNA SPIN kit for soil” (MP Biomedicals, Illkirch, France). The extraction included two bead beating steps of 45 s at 6.5 m s-1 on a FastPrep-24 system (MP Biomedicals) and additional washing steps of the binding matrix each with 1 ml 5.5 M guanidine thiocyanate (Carl Roth GmbH) until the matrix retained its original color (1 - 3 washes).

text: soil

characteristic: enviornmental package

text: field soil; ENVO:00005755

characteristic: environment (featurel)

text: rhizosphere; ENVO:00005801

characteristic: environment (material)

text: 52° N

characteristic: geographic location (latitude)

text: 10° E

characteristic: geographic location (longitude)

text: MIMARKS

characteristic: investigation type

characteristic: nucleic acid extraction

text: rhizosphere metagenome

characteristic: organism

characteristic: pcr conditions

text: F_Com1_MID13: ccatctcatccctgcgtgtctccgactcagCATAGTAGTGCAGCAGCCGCGGTAATAC; R_Com2: cctatcccctgtgtgccttggcagtctcagCCGTCAATTCCTTTGAGTTT

characteristic: pcr primers

text: maize rhizosphere

text: rhizosphere metagenome

text: Pyrosequencing

text: 16S rRNA

characteristic: title


text: GSC:MIxS v2.1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: GSC, MIxS

characteristic: ENA-KEYWORD

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Germany, Lower Saxony

text: VTI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: BBCH 63 - 65; August 2009

text: maize culticar Benicia

text: 2-15 cm

characteristic: description

text: soil

text: field soil; ENVO:00005755

text: rhizosphere; ENVO:00005801

text: 52° N

text: 10° E

text: MIMARKS

text: rhizosphere metagenome

text: F_Com1_MID1: ccatctcatccctgcgtgtctccgactcagACGAGTGCGTCAGCAGCCGCGGTAATAC; R_Com2: cctatcccctgtgtgccttggcagtctcagCCGTCAATTCCTTTGAGTTT

characteristic: ph

text: maize rhizosphere

characteristic: project name

text: rhizosphere metagenome

text: Pyrosequencing

text: 16S rRNA

text: Rhizosphere microbial communities were extracted by saline washes of fine roots (diameter >1mm) of maize cultivar Benicia, collected at the flowering stage BBCH 63-65. Individual plants were sampled. Total DNA was extracted from the collected cells by “FastDNA SPIN kit for soil” (MP Biomedicals, Illkirch, France). The extraction included two bead beating steps of 45 s at 6.5 m s-1 on a FastPrep-24 system (MP Biomedicals) and additional washing steps of the binding matrix each with 1 ml 5.5 M guanidine thiocyanate (Carl Roth GmbH) until the matrix retained its original color (1 - 3 washes).


text: GSC:MIxS v2.1

text: GSC, MIxS

text: Germany, Lower Saxony

text: VTI

text: public

text: BBCH 63 - 65; August 2009

characteristic: collection date

text: maize culticar 3BT

characteristic: current vegetation

text: 2-15 cm

characteristic: depth

text: soil

characteristic: enviornmental package

text: field soil; ENVO:00005755

characteristic: environment (featurel)

text: rhizosphere; ENVO:00005801

characteristic: environment (material)

text: 52° N

characteristic: geographic location (latitude)

text: 10° E

characteristic: geographic location (longitude)

text: MIMARKS

characteristic: investigation type

text: “FastDNA SPIN kit for soil” (MP Biomedicals, Illkirch, France)

characteristic: nucleic acid extraction

text: rhizosphere metagenome

characteristic: organism

characteristic: pcr conditions

text: F_Com1_MID8:ccatctcatccctgcgtgtctccgactcagCTCGCGTGTCCAGCAGCCGCGGTAATAC; R_Com2: cctatcccctgtgtgccttggcagtctcagCCGTCAATTCCTTTGAGTTT

text: maize rhizosphere

text: rhizosphere metagenome

text: Pyrosequencing

characteristic: sequencing method

text: 16S rRNA

characteristic: target gene


text: GSC:MIxS v2.1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: GSC, MIxS

characteristic: ENA-KEYWORD

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Germany, Lower Saxony

text: VTI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: BBCH 63 - 65; August 2009

text: maize culticar DKC 4250

text: 2-15 cm

characteristic: description

text: soil

text: field soil; ENVO:00005755

text: rhizosphere; ENVO:00005801

text: 52° N

text: 10° E

text: MIMARKS

text: rhizosphere metagenome

text: F_Com1_MID3: ccatctcatccctgcgtgtctccgactcagAGACGCACTCCAGCAGCCGCGGTAATAC; R_Com2: cctatcccctgtgtgccttggcagtctcagCCGTCAATTCCTTTGAGTTT

characteristic: pcr primers

text: maize rhizosphere

text: rhizosphere metagenome

text: Pyrosequencing

text: 16S rRNA

characteristic: title


text: GSC:MIxS v2.1

text: GSC, MIxS

text: Germany, Lower Saxony

text: VTI

text: public

text: BBCH 63 - 65; August 2009

characteristic: collection date

text: maize culticar 3BT

characteristic: current vegetation

text: 2-15 cm

characteristic: depth

text: Rhizosphere microbial communities were collected by saline washes of coarse roots (diameter 2-4 mm) of maize cultivar 3BT, collected at the flowering stage BBCH 63-65. Total DNA was extracted from the collected cells by “FastDNA SPIN kit for soil” (MP Biomedicals, Illkirch, France). The extraction included two bead beating steps of 45 s at 6.5 m s-1 on a FastPrep-24 system (MP Biomedicals) and additional washing steps of the binding matrix each with 1 ml 5.5 M guanidine thiocyanate (Carl Roth GmbH) until the matrix retained its original color (1 - 3 washes).

text: soil

characteristic: enviornmental package

text: field soil; ENVO:00005755

characteristic: environment (featurel)

text: rhizosphere; ENVO:00005801

characteristic: environment (material)

text: 52° N

characteristic: geographic location (latitude)

text: 10° E

characteristic: geographic location (longitude)

text: MIMARKS

characteristic: investigation type

characteristic: nucleic acid extraction

text: rhizosphere metagenome

characteristic: organism

characteristic: pcr conditions

text: F_Com1_MID11: ccatctcatccctgcgtgtctccgactcagTGATACGTCTCAGCAGCCGCGGTAATAC; R_Com2: cctatcccctgtgtgccttggcagtctcagCCGTCAATTCCTTTGAGTTT

characteristic: ph

text: maize rhizosphere

characteristic: project name

text: rhizosphere metagenome

text: Pyrosequencing

text: 16S rRNA


text: Clostridium indolis

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: intest004-sc-2012-01-12T11:15:30Z-1331364

characteristic: Submitter Id

text: [Clostridium] indolis

text: [Clostridium] indolis


text: Clostridium indolis

text: SC

text: public

text: intest013-sc-2012-01-12T11:15:49Z-1331373

text: [Clostridium] indolis

text: [Clostridium] indolis


text: Blautia coccoides

text: SC

text: public

text: intest016-sc-2012-01-12T11:15:50Z-1331376

text: Blautia coccoides

text: Blautia coccoides


text: Enterococcus hirae

text: SC

text: public

text: intest007-sc-2012-01-12T11:15:44Z-1331367

text: Enterococcus hirae

text: Enterococcus hirae


text: Staphylococcus warneri

text: SC

text: public

text: intest012-sc-2012-01-12T11:15:48Z-1331372

text: Staphylococcus warneri

text: Staphylococcus warneri


text: Enterococcus hirae

text: SC

text: public

text: intest008-sc-2012-01-12T11:15:45Z-1331368

text: Enterococcus hirae

text: Enterococcus hirae


text: Enterococcus durans

text: SC

text: public

text: intest009-sc-2012-01-12T11:15:46Z-1331369

text: Enterococcus durans

text: Enterococcus durans


text: Enterorhabdus mucosicola

text: SC

text: public

text: intest015-sc-2012-01-12T11:50:46Z-1331375

text: Enterorhabdus mucosicola

text: Enterorhabdus mucosicola


text: Adlercreutzia equolifaciens

text: SC

text: public

text: intest014-sc-2012-01-12T11:15:50Z-1331374

text: Adlercreutzia equolifaciens

text: Adlercreutzia equolifaciens


text: Staphylococcus

text: SC

text: public

text: intest003-sc-2012-01-12T11:50:44Z-1331363

text: Staphylococcus

text: Staphylococcus


text: Staphylococcus pasteuri

text: SC

text: public

text: intest011-sc-2012-01-12T11:15:47Z-1331371

text: Staphylococcus pasteuri

text: Staphylococcus pasteuri


text: Enterococcus

text: SC

text: public

text: intest001-sc-2012-01-12T11:50:43Z-1331361

text: Enterococcus

text: Enterococcus


text: Barnesiella intestinihominis

text: SC

text: public

text: intest006-sc-2012-01-12T11:15:43Z-1331366

text: Barnesiella intestinihominis

text: Barnesiella intestinihominis


text: Adlercreutzia equolifaciens

text: SC

text: public

text: intest005-sc-2012-01-12T11:15:31Z-1331365

text: Adlercreutzia equolifaciens

text: Adlercreutzia equolifaciens


text: Lactobacillus reuteri

text: SC

text: public

text: intest002-sc-2012-01-12T11:15:28Z-1331362

text: Lactobacillus reuteri

text: Lactobacillus reuteri


text: Lactobacillus reuteri

text: SC

text: public

text: intest010-sc-2012-01-12T11:15:47Z-1331370

text: Lactobacillus reuteri

text: Lactobacillus reuteri


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: MPI-PZ

text: public

text: mRNA fraction extracted from infected Arabidopsis thaliana leaves containing mRNAs from Golovinomyces and Arabidopsis

characteristic: description

text: Golovinomyces orontii

text: Golovinomyces orontii

text: G. orontii haustoria ESTs.

characteristic: title


text: SRA-Webin

text: MPI-PZ

text: public

text: Golovinomyces orontii

characteristic: organism

text: Golovinomyces orontii

text: genomic sequence


text: SRA-Webin

text: MPI-PZ

text: public

text: Golovinomyces orontii

text: Golovinomyces orontii

text: G. orontii genomic sequences


text: BGI-Shenzhen, Shenzhen, China.

text: public

text: 3 years

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Chinese brown frog

characteristic: common name

text: Protocols: Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's instructions.

text: hibernation period

characteristic: developmental stage

text: Rana chensinensis

text: Rana chensinensis

text: oviduct

characteristic: organism part

text: Rana chensinensis

text: female

characteristic: sex


text: GSC:MIxS v2.1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: GSC, MIxS, MIMARKS

characteristic: ENA-KEYWORD

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Norway

text: CGG-UCop

text: public

text: Pyrosequencing

characteristic: Sequencing method

unit: g

characteristic: amount or size of sample collected

characteristic: collection date

characteristic: depth

text: Lake sediment samples taken from core (1 cm per sample). Extraction, PCR

text: sediment

characteristic: enviornmental package

text: Freshwater biome. ENVO:00000873

characteristic: environment (biome)

text: Fresh water habitat ENVO:00002037

characteristic: environment (featurel)

text: Lake sediment. ENVO:00000546

characteristic: environment (material)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: MIxS

characteristic: investigation type

text: sediment metagenome

text: Initial denaturation:94degC_4min; Denaturation:94degC_45sec; Annealing:55-57degC_45sec; Extension:68degC_45sec; Cycles:55-60; Final elongation:70degC_10min. Final hold:4degC_forever

characteristic: pcr conditions

text: trnL_g: GGGCAATCCTGAGCCAA; trnL_h: CCATTGAGTCTCTGCACCTATC

characteristic: pcr primers

text: Sequences Andøya

characteristic: project name

characteristic: sample storage temperature

text: sediment metagenome

text: Pyrosequencing

characteristic: sequencing method

text: trnL

characteristic: target gene


And�ya_extraction blank

text: GSC:MIxS v2.1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: GSC, MIxS, MIMARKS

characteristic: ENA-KEYWORD

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CGG-UCop

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Pyrosequencing

characteristic: Sequencing method

text: And�ya_extraction blank

characteristic: Submitter Id

characteristic: description

text: sediment

text: MIxS

text: sediment metagenome

characteristic: organism

text: Sequences Andøya

text: sediment metagenome

text: Pyrosequencing

text: trnL

text: Andoya_extraction blank

characteristic: title


text: SRA-Webin

characteristic: ENA-SUBMISSION-TOOL

text: DPSQ

text: public

text: Roche 454 FLX reads of cDNA generated from P. hawaiensis embryo samples.

text: Parhyale hawaiensis

text: Parhyale hawaiensis

text: P. hawaiensis 454 cDNA reads from embryo samples


Verruco AAA168-E21_illumina

text: SRA-Webin

text: GSG-LANL

text: public

text: Verruco AAA168-E21_illumina

text: Surface water samples were collected from the Gulf of Maine (43�50_40__N 69�38_27__W) and the freshwater, mesotrophic Damariscotta Lake (44�10'38N 69�29'12W) in Maine, USA, on July 19, 2009 and analyzed within two hours of storage at in situ temperature in the dark. Water samples were pre-screened through a 70 �m mesh-size cell strainer (BD) and the bacterioplankton cells were labeled, in parallel, using different fluorescent probes, for subsequent single cell sorting, DNA extraction, amplification and sequencing. Whole genome sequencing was accomplished using a hybrid approach, combining Illumina short read data with PacBio long read data.

text: Verrucomicrobia bacterium SCGC AAA168-E21

text: Genomic sequencing of selected Verrucomicrobia cells AAA168-E21


Verruco AAA168-E21_pacbio

text: SRA-Webin

text: GSG-LANL

text: public

text: Verruco AAA168-E21_pacbio

text: Surface water samples were collected from the Gulf of Maine (43�50_40__N 69�38_27__W) and the freshwater, mesotrophic Damariscotta Lake (44�10'38""N 69�29'12""W) in Maine, USA, on July 19, 2009 and analyzed within two hours of storage at in situ temperature in the dark. Water samples were pre-screened through a 70 �m mesh-size cell strainer (BD) and the bacterioplankton cells were labeled, in parallel, using different fluorescent probes, for subsequent single cell sorting, DNA extraction, amplification and sequencing. Whole genome sequencing was accomplished using PacBio long read data.


Verruco AAA164-O14_illumina

text: SRA-Webin

text: GSG-LANL

text: public

text: Verruco AAA164-O14_illumina

text: Verrucomicrobia bacterium SCGC AAA164-O14

text: Genomic sequencing of selected Verrucomicrobia cells AAA164-O14


Verruco AAA164-L15_illumina

text: SRA-Webin

text: GSG-LANL

text: public

text: Verruco AAA164-L15_illumina

text: Verrucomicrobia bacterium SCGC AAA164-L15

text: Genomic sequencing of selected Verrucomicrobia cells AAA164-L15


Verruco AAA164-L15_pacbio

text: SRA-Webin

text: GSG-LANL

text: public

text: Verruco AAA164-L15_pacbio


Verruco AAA164-O14_pacbio

text: SRA-Webin

text: GSG-LANL

text: public

text: Verruco AAA164-O14_pacbio


Verruco AAA164-A21_illumina

text: SRA-Webin

text: GSG-LANL

text: public

text: Verruco AAA164-A21_illumina

text: Verrucomicrobia bacterium SCGC AAA164-A21

text: Genomic sequencing of selected Verrucomicrobia cells AAA164-A21


Verruco AAA168-F10_illumina

text: SRA-Webin

text: GSG-LANL

text: public

text: Verruco AAA168-F10_illumina

text: Verrucomicrobia bacterium SCGC AAA168-F10

text: Genomic sequencing of selected Verrucomicrobia cells AAA168-F10


Verruco AAA164-A21_pacbio

text: SRA-Webin

text: GSG-LANL

text: public

text: Verruco AAA164-A21_pacbio


E-MTAB-75:Cell culture 1

text: Institut Pasteur

text: public

characteristic: StrainOrLine

text: E-MTAB-75:Cell culture 1

tag: Namespace:Institut Pasteur

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: Protocols: Cells were grown to mid-exponential phase in YPD for a wild type strain (condion 1) and in YPD supplemented with doxycycline (10µg/ml) for 16h for the mutant strain (condition 2).

text: MAT_ ura3_0 leu2_0 his3_1 lys2_0

characteristic: genotype

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Cell culture 1


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CRUK-CRI

text: public

text: ArrayExpress

text: LNCAP

characteristic: cell line

text: epithelial

characteristic: cell type

text: human

text: Protocols: MDA-MB-453 and MCF7 cells were grown in DMEM containing 10% heat-inactivated FBS, 2 mM L glutamine, 50 U/ml penicillin and 50 ug/ml streptomycin and LNCaP cells were grown in RPMI containing 10% heat-inactivated FBS, 2 mM L glutamine, 50 U/ml penicillin and 50 ug/ml streptomycin. The antibodies used were anti-AR (sc-816) and anti-ER (sc-543) from Santa Cruz Biotechnologies and anti-FoxA1 (ab5089) from Abcam. Four 15 cm dishes of cells were used per chromatin immunoprecipitation (ChIP) and samples were processed according to standard ChIP procedures as described in Schmidt et al, Methods 48(3) July 2009 doi:10.1016/j.ymeth.2009.03.001. The immunoprecipitated DNA was subsequently amplified as previously described for Illumina sequencing (Schmidt et al, 2009).

text: Homo sapiens

text: Homo sapiens

text: prostate

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: LNCaP


characteristic: External Id

text: CRUK-CRI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: epithelial

text: human

text: Homo sapiens

text: Homo sapiens

text: breast

text: Homo sapiens

text: female


text: Anopheles gambiae

characteristic: ArrayExpress-Species

text: SC

text: public

characteristic: Submitter Id

text: African malaria mosquito

text: Anopheles gambiae

characteristic: organism

text: Anopheles gambiae


text: SC

text: public

text: house mouse

characteristic: common name

text: F1_me3_B2 H3K4me3

characteristic: description

text: Mus musculus

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: sample description

text: Mus musculus

characteristic: strain


characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: N2me1D1 H3K4me1

text: Mus musculus

text: Mus musculus


text: SC

text: public

text: house mouse

text: N2inputF2 Input

text: Mus musculus

text: Mus musculus


text: SC

text: public

text: house mouse

text: N2_me3_B2 H3K4me3

text: Mus musculus

text: Mus musculus


text: SC

text: public

text: house mouse

text: F1me1B1 H3K4me1

text: Mus musculus

text: Mus musculus


text: SC

text: public

text: house mouse

text: N2inputB2 Input

text: Mus musculus

text: Mus musculus


text: SC

text: public

text: house mouse

text: F1_me3_D2 H3K4me3

text: Mus musculus

text: Mus musculus


text: SC

text: public

text: house mouse

text: N2_me3_D2 H3K4me3

text: Mus musculus

text: Mus musculus


text: Sus scrofa

text: SC

text: public

text: WTSI_1061_50K3-sc-2012-03-09T13:58:25Z-1150497

text: pig

text: Sus scrofa

text: Sus scrofa


text: Sus scrofa

text: SC

text: public

text: WTSI_1061_28O20-sc-2012-03-09T13:55:23Z-1136887

text: pig

text: Sus scrofa

text: Sus scrofa


text: Sus scrofa

text: SC

text: public

text: CH242_360J12-sc-2012-03-09T13:52:23Z-1123877

text: pig

text: Sus scrofa

text: Sus scrofa


text: Sus scrofa

text: SC

text: public

text: WTSI_1061_55E17-sc-2012-03-09T14:03:33Z-1248768

text: pig

text: Sus scrofa

text: Sus scrofa


text: Sus scrofa

text: SC

text: public

text: WTSI_1061_81P14-sc-2012-03-09T14:01:04Z-1164260

text: pig

text: Sus scrofa

text: Sus scrofa


text: Sus scrofa

text: SC

text: public

text: WTSI_1061_24O15-sc-2012-03-09T14:01:58Z-1197943

text: pig

text: Sus scrofa

text: Sus scrofa


text: Sus scrofa

text: SC

text: public

text: WTSI_1061_35M24-sc-2012-03-09T13:51:04Z-1069009

text: pig

text: Sus scrofa

text: Sus scrofa


text: Sus scrofa

text: SC

text: public

text: WTSI_1061_66E18-sc-2012-03-09T13:59:22Z-1164131

text: pig

text: Sus scrofa

text: Sus scrofa


text: Sus scrofa

text: SC

text: public

text: WTSI_1061_24P18-sc-2012-03-09T14:01:59Z-1197944

text: pig

text: Sus scrofa

text: Sus scrofa


text: Sus scrofa

text: SC

text: public

text: WTSI_1061_42C16-sc-2012-03-09T13:57:14Z-1150412

text: pig

text: Sus scrofa

text: Sus scrofa


text: Sus scrofa

text: SC

text: public

text: WTSI_1061_4C16-sc-2012-03-09T13:53:06Z-1123928

text: pig

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