text: Instituto Gulbenkian de Ciencia

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Instituto Gulbenkian de Ciencia

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: neural stem cell

characteristic: cell type

text: house mouse

text: Protocols: NS5 cells were cultured as previously described (Conti et al. 2005), using laminin as a media supplement (20ug/mL), and plated at a density of 28,000/cm2 NS5 cells were infected with pBABE-Ascl1-ERT2-IRES-GFP-puro (NS5_Ascl1), followed by selection in complete medium containing 1ug/mL puromycin (Calbiochem), and collected 30 minutes after induction with 4-Hydroxytamoxifen at a final concentration of 50nM, while reducing EGF concentration to 5ng/ml NS cells were fixed sequentially with di(N-succimidyl) glutarate and 1% formaldehyde in phosphate buffered saline and then lysed, sonicated and immunoprecipitated, as previously described (Castro et al., 2011), with rabbit anti-HA (ab1424, Abcam) DNA libraries were prepared from 10ng of immunoprecipitated DNA according to the standard Illumina ChIP-seq protocol.

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DKFZ

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: ArrayExpress

text: granulocyte

text: human

characteristic: common name

text: Protocols: HL-60/S4 cells were cultured in RPMI-1640 medium with 10% heat-inactivated fetal calf serum and 1% penicillin/streptomycin. Cells were differentiated into granulocytes by addition of all-trans ratinoic acid and into macrophage by phorbol ester. Cells were fixed, lysed and incubated with primary antibody, either PL2-6 or 1H6, before they were fixed again and sonicated in Covaris micro-chambers. The harvested supernatant was incubated with Protein A/G agarose to bind the epichromatin-antibody complex, and the remainder (input) represents the total nuclear chromatin. The epichromatin (IP) was eluted from the complex. DNA was purified with QIAquick PCR Purification Kit (QIAGEN). ChIP-seq libraries were prepared with NEB Next Chip Seq DNA Sample Prep Kit according to the manufacturers protocol.

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

characteristic: title

type: has member


text: DKFZ

text: public

characteristic: INSDC status

text: ArrayExpress

text: undifferentiated myeloid leukemic cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: DKFZ

text: public

characteristic: SRA accession

text: ArrayExpress

text: macrophage

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


E-MTAB-2383:4T1-luc2-tdTomato rep2

text: TRON

text: public

text: E-MTAB-2383:4T1-luc2-tdTomato rep2

text: ArrayExpress

characteristic: broker name

text: breast tumor cell

text: house mouse

text: Protocols: 4T1 breast tumor cells were purchased from Caliper Life Sciences (product 125669). The samples have been transfected with Luciferase/Tomato Replicate exome capture for DNA resequencing was performed using the Agilent Sure-Select mouse whole-exome solution-based capture assay Oligo (dT) RNA was isolated from each tumor cell line (B16F10, CT26 and 4T1) in replicate and was prepared for gene expression profiling

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

text: 4T1-luc2-tdTomato rep2


E-MTAB-2383:4T1-luc2-tdTomato rep1

text: TRON

text: public

text: E-MTAB-2383:4T1-luc2-tdTomato rep1

text: ArrayExpress

characteristic: cell line

text: breast tumor cell

characteristic: cell type

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

text: 4T1-luc2-tdTomato rep1


E-MTAB-2383:4T1-luc2-tdTomato rep3

characteristic: ENA-CHECKLIST

text: TRON

text: public

text: E-MTAB-2383:4T1-luc2-tdTomato rep3

text: ArrayExpress

text: breast tumor cell

text: house mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: fresh specimen

text: 4T1-luc2-tdTomato rep3


characteristic: ArrayExpress-CellType

text: Blood

characteristic: ArrayExpress-OrganismPart

text: Cancer

characteristic: ArrayExpress-Phenotype

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: human

text: Homo sapiens

characteristic: sample description

text: Homo sapiens


characteristic: ArrayExpress-Immunoprecipitate

text: Blood

text: Cancer

text: female

text: Homo sapiens

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: Blood

text: Cancer

text: male

text: Homo sapiens

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human

text: Homo sapiens

text: Homo sapiens


characteristic: ArrayExpress-CellType

text: CEBPE

text: Blood

characteristic: ArrayExpress-OrganismPart

text: Cancer

characteristic: ArrayExpress-Phenotype

text: female

text: Homo sapiens

text: SC

text: public

text: human

text: Homo sapiens

text: CEBPE-ChIPseq

text: Homo sapiens


text: Input

text: Blood

text: Cancer

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: human

text: Homo sapiens

text: WCE-ChIPseq

text: Homo sapiens


text: CTCF

characteristic: ArrayExpress-Immunoprecipitate

text: Blood

text: Cancer

text: female

text: Homo sapiens

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: human

text: Homo sapiens

text: CTCF

characteristic: sample description

text: Homo sapiens


text: CTCF

text: Blood

text: Cancer

text: male

text: Homo sapiens

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human

text: Homo sapiens

text: CTCF

text: Homo sapiens


E-MTAB-2350:B63 Dif

characteristic: INSDC last update

text: public

text: E-MTAB-2350:B63 Dif

tag: Namespace:University of Pennsylvania, School of Medicine, Dept. of Genetics

characteristic: Submitter Id

text: 3 month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: differentiated intestinal epithelium

characteristic: cell type

text: house mouse

characteristic: common name

text: Protocols: All procedures involving mice were conducted in accordance with approved Institutional Animal Care and Use Committee protocols. WGSBS was performed as previously published (Lister, Nature 462: 315-322) with the following changes. Isolated genomic DNA was fragmented into 300bp pieces using the S220 Focused - ultrasonicator (Covaris). Sequencing libraries were generated with 500ng genomic DNA using the NEBNext genomic sequencing kit (NEB) and Illumina adaptors (PE-102-1001. PE-102- 1002). Libraries were bisulfite converted using Imprint DNA Modification Kit (Sigma). Size selection of the libraries to 300-600bp was performed on the Pippin Prep DNA size selection system (Sage Science). Amplification of libraries was performed in 18 rounds of PCR using Pfu Turbo Cx Hotstart DNA Polymerase (Agilent Technologies).

characteristic: description

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: small intestine

characteristic: organism part

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

text: C57Bl/6 background Lgr5-EGFP-ires-CreERT2

characteristic: strain

text: B63 Dif

characteristic: title


E-MTAB-2350:1 Diff-K27ac-1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Pennsylvania, School of Medicine, Dept. of Genetics

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2350:1 Diff-K27ac-1

text: 3 month

text: ArrayExpress

text: differentiated intestinal epithelium

text: house mouse

text: Protocols: All procedures involving mice were conducted in accordance with approved Institutional Animal Care and Use Committee protocols. LGR5+ and differentiated cells were isolated and incubated in 1.11% formaldehyde for 10 minutes at room temperature. Chromatin was sonicated into 200 to 300bp fragments using the BioRuptor (Diagenode). ChIP-Seq libraries were made using the ChIP-Seq Library Prep Reagent Set (NEB). Immunoprecipitation was performed using 2ug H3K27ac antibody (Active Motif) and 2ug of chromatin for two biological replicates for each cell type.

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: small intestine

text: Mus musculus

text: fresh specimen

text: 1 Diff-K27ac-1


E-MTAB-2350:31 LGR5-K27ac-31

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-2350:31 LGR5-K27ac-31

characteristic: Submitter Id

text: 3 month

text: ArrayExpress

text: intestinal stem cell (LGR5 positive)

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: small intestine

text: Mus musculus

text: fresh specimen

text: 31 LGR5-K27ac-31


E-MTAB-2350:34 LGR5-K27ac-34

text: public

text: E-MTAB-2350:34 LGR5-K27ac-34

text: 3 month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: intestinal stem cell (LGR5 positive)

characteristic: cell type

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: Mus musculus

text: Mus musculus

text: small intestine

text: Mus musculus

text: fresh specimen

text: 34 LGR5-K27ac-34


E-MTAB-2350:B62 Dif

text: public

text: E-MTAB-2350:B62 Dif

text: 3 month

text: ArrayExpress

text: differentiated intestinal epithelium

text: house mouse

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: small intestine

characteristic: organism part

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain

text: B62 Dif

characteristic: title


E-MTAB-2350:6 Diff-K27ac-6

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2350:6 Diff-K27ac-6

text: 3 month

text: ArrayExpress

text: differentiated intestinal epithelium

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: small intestine

text: Mus musculus

text: fresh specimen

text: 6 Diff-K27ac-6


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 3 month

text: ArrayExpress

text: differentiated intestinal epithelium

text: house mouse

text: Protocols: All procedures involving mice were conducted in accordance with approved Institutional Animal Care and Use Committee protocols. RNA was extracted from cells using the Qiagen AllPrep DNA/RNA Mini Kit RNA sequencing libraries were constructed from 200ug total RNA isolated using TruSeq RNA Sample Prep Kit (Illumina).

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: small intestine

text: Mus musculus

text: fresh specimen

text: dif-mRNA


E-MTAB-2350:20120920 LGR5_611

text: public

text: E-MTAB-2350:20120920 LGR5_611

characteristic: Submitter Id

text: 3 month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: intestinal stem cell (LGR5 positive)

characteristic: cell type

text: house mouse

characteristic: common name

text: adult

text: Mus musculus

text: Mus musculus

text: small intestine

text: Mus musculus

text: fresh specimen

text: 20120920 LGR5_611


text: public

text: 3 month

text: ArrayExpress

text: intestinal stem cell (LGR5 positive)

text: house mouse

characteristic: description

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: small intestine

characteristic: organism part

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain


E-MTAB-2350:2 LGR5_GFP

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

text: E-MTAB-2350:2 LGR5_GFP

text: 3 month

text: ArrayExpress

text: intestinal stem cell (LGR5 positive)

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: small intestine

text: Mus musculus

text: fresh specimen

text: 2 LGR5_GFP

characteristic: title


E-MTAB-2350:11/7/12 5

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-2350:11/7/12 5

text: 3 month

text: ArrayExpress

text: differentiated intestinal epithelium

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: small intestine

text: Mus musculus

text: fresh specimen

text: 11/7/12 5


text: public

characteristic: Submitter Id

text: 3 month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: differentiated intestinal epithelium

characteristic: cell type

text: house mouse

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: small intestine

text: Mus musculus

text: fresh specimen


E-MTAB-2350:B61 Dif

text: public

text: E-MTAB-2350:B61 Dif

text: 3 month

text: ArrayExpress

text: differentiated intestinal epithelium

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: small intestine

characteristic: organism part

text: Mus musculus

text: fresh specimen

characteristic: specimen with known storage state

text: B61 Dif


E-MTAB-2350:1 LGR5_GFP

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

text: E-MTAB-2350:1 LGR5_GFP

text: 3 month

text: ArrayExpress

text: intestinal stem cell (LGR5 positive)

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: small intestine

text: Mus musculus

text: fresh specimen

characteristic: strain

text: 1 LGR5_GFP


E-MTAB-2350:3 LGR5_GFP

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-2350:3 LGR5_GFP

text: 3 month

text: ArrayExpress

text: intestinal stem cell (LGR5 positive)

text: house mouse

text: adult

text: Mus musculus

text: Mus musculus

text: small intestine

text: Mus musculus

text: fresh specimen

text: 3 LGR5_GFP

characteristic: title


text: University of Edinburgh

text: public

characteristic: SRA accession

tag: Namespace:University of Edinburgh

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: sheep

text: Protocols: New Zealand Cheviot sheep of PRNP genotypes VRQ/VRQ, from the DEFRA breeding flock were inoculated subcutaneously with 2 ml of 10% w/v brain homogenate into sites on either side of the neck roughly 10cm anterior to the prescapular lymph node (PSLN). In all experiments frozen lymph node was converted to a frozen tissue powder. Briefly a 100 mg of tissue per sample was placed into a Teflon flask along with steel ball and placed in liquid Nitrogen for 1 min. Homogenised for 60 seconds at 2000 rpm in a Mikro-Dismembrator U (B.Braun Biotech International GmbH). Total RNA was extracted from the frozen tissue powder using the RiboPure Kit (Ambion) including a DNase I digestion. To the frozen tissue powder 1 ml of Tri Reagent was added and then homogenise for a further 15 seconds at 1500rpm. A 200 ul aliquot of chloroform was added to lysate and mixed vigorously by vortexing. The protocol was then followed as per the manufactures instructions. The RNA was eluted in a final volume of 50 ul. Each RNA sample was DNase I (Ambion) treated as per the manufacturers instructions. The quality and quantity of the isolated total RNA was assessed using a RNA LabChip on the Agilent 2100 bioanalyser and a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies Inc.). (

text: lamb

text: standard scrapie sheep prion (SSBP/1) infected

characteristic: disease

text: Ovis aries

text: Ovis aries

text: Obex

text: Ovis aries

text: Male

characteristic: sex

text: frozen specimen


text: University of Edinburgh

text: public

text: ArrayExpress

text: sheep

characteristic: common name

characteristic: description

text: lamb

characteristic: developmental stage

text: mock infected

text: Ovis aries

characteristic: organism

text: Ovis aries

text: Obex

characteristic: organism part

text: Ovis aries

text: Male

text: frozen specimen


text: Danio rerio

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: genomic DNA

characteristic: sample description

text: Danio rerio


E-MTAB-2264:cumulus oophorus cells

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-2264:cumulus oophorus cells

tag: Namespace:University of Science of Technology of China

text: 29 hour

characteristic: age

text: ArrayExpress

text: normal

characteristic: cell type

text: cumulus oophorus cells

text: human

text: Protocols: Briefly, the cumulus' oocyte complexes were retrieved 36 h after hCG treatment and washed in multiple dishes with Flushing medium (William A. Cook Australia Pty. Ltd, Queensland, Australia). The cumulus oophorus cells were collected in the fertilization medium (William A. Cook Australia Pty. Ltd, Queensland, Australia) by two disposable needles and two 1-ml plastic disposable syringes without hyaluronidase. To avoid the interfusion of corona radiata cells, the innermost layers of cumulus oophorus cells were not collected. On the other hand, the corona radiata cells were collected as described in our previous publication and other reports. The corona radiata cells separated from the oocyte by gentle pipetting with a 135 mm diameter stripper pipette and micromanipulator System. MII oocytes were used for ICSI procedure. The corona radiata cells and cumulus oophorus cells were pooled by centrifuging at 1500g for 8 min, and immediately frozen in liquid nitrogen until use All the five patients were stimulated with the standard long gonadotrophin-releasing hormone agonist (GnRHa, Diphereline; Ipsen Pharma. Biotech, Signes, France) protocol combined with the administration of recombinant FSH (Gonal-f, Merk Serono SA, Geneva, Switzerland). For oocyte retrieve, all patients underwent ovarian puncture (OPU) of follicles larger than 15 mm after 36 h of administration of 10 000 IU human chorionic gonadotrophin (hCG, LiZhu Pharma, ZhuHai, China). Only the cumulus'oocyte complexs with Metaphase II (MII) oocytes were included in this study. Total RNAs were extracted from the human CRCs and COCs using TRIzol reagents (Invitrogen). Library preparation and sequencing was performed at BGI-Shenzhen.

text: pool cells from five patients

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

text: fresh specimen

characteristic: specimen with known storage state

text: cumulus oophorus cells

characteristic: title


E-MTAB-2264:corona radiata cells

text: University of Science of Technology of China

text: public

characteristic: SRA accession

text: E-MTAB-2264:corona radiata cells

characteristic: Submitter Id

text: 29 hour

text: ArrayExpress

characteristic: broker name

text: normal

text: corona radiata cells

text: human

characteristic: common name

characteristic: description

text: pool cells from five patients

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex

text: fresh specimen

text: corona radiata cells


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: GSC

text: public

characteristic: INSDC status

text: rape

text: Brassica napus

text: Brassica napus

text: Brassica napus (Darmor-Bzh genotype)


characteristic: External Id

text: GSC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: rape

text: Brassica napus

text: Brassica napus

text: Brassica napus (Yudal genotype)


text: Danio rerio

characteristic: ArrayExpress-Species

text: SC

text: public

text: zebrafish

text: Danio rerio

text: Danio rerio


text: TelAML1/+, Pax5+/-

characteristic: ArrayExpress-Genotype

text: Spleen

characteristic: ArrayExpress-OrganismPart

text: Cancer

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: RNA from spleen

characteristic: sample description

text: Mus musculus


text: TelAML1/+, Pax5+/-

text: Spleen

text: Cancer

text: female

text: Mus musculus

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: RNA from spleen

text: Mus musculus


text: TelAML1/+, Pax5+/-

text: Spleen

text: Healthy (control)

text: female

text: Mus musculus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: RNA from spleen

text: Mus musculus


text: TelAML1/+, Pax5+/-

text: Spleen

text: Healthy (control)

text: male

text: Mus musculus

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: RNA from spleen

text: Mus musculus


characteristic: External Id

text: University of Oxford

text: public

characteristic: INSDC status

tag: Namespace:University of Oxford

text: ArrayExpress

characteristic: broker name

text: monocyte

characteristic: cell type

text: human

text: Protocols: Monocytes were separated with the Miltenyi Monocyte Isolation kit II (Miltenyi biotec) and re-suspended in RPMI 1640 medium (supp. 2 mM L-glutamine 10,000 U/mL penicillin 10 mg/mL streptomycin and 10% (v/v) fetal bovine serum (Invitrogen, Paisley, UK)) Experimental samples were treated with 10ng/ml LPS for 4 hours and the controls were left untreated (n = 4 per group). Total RNA was extracted using the Qiagen RNeasy kit and included an on-column DNase treatment Ribosomal RNA (rRNA) was depleted using an early-access version of the Ribo-Zero Gold rRNA Removal Kit (Epicentre). Strand-specific cDNA libraries were prepared using an early-access version of the ScriptSeq v2 library preparation kit (Epicentre)

characteristic: description

text: PeF-LPS

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen

characteristic: specimen with known storage state

characteristic: title


text: University of Oxford

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: monocyte

text: human

text: LoD-NS

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen


text: University of Oxford

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: monocyte

text: human

text: CaT-NS

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen


characteristic: ENA-CHECKLIST

text: University of Oxford

text: public

text: ArrayExpress

text: monocyte

text: human

characteristic: common name

text: LoD-LPS

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen


characteristic: ENA-FIRST-PUBLIC

text: University of Oxford

text: public

text: ArrayExpress

text: monocyte

text: human

text: PeF-NS

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: fresh specimen


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oxford

text: public

text: ArrayExpress

text: monocyte

text: human

text: DaG-LPS

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen


text: University of Oxford

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: monocyte

text: human

text: DaG-NS

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen


text: University of Oxford

text: public

text: ArrayExpress

text: monocyte

characteristic: cell type

text: human

characteristic: description

text: CaT-LPS

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: fresh specimen


text: UNIVERSITY OF MANCHESTER

text: public

tag: Namespace:UNIVERSITY OF MANCHESTER

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: U2OS cells, were grown in DMEM supplemented with 10% foetal bovine serum. ChIP was performed as previously described (Marais et al., 2010) using ~8-10 x 10+7 U2OS-FOXK2-HF cells stably expressing FOXK2 tagged with Flag and His tags (~4Ã-150 mm plates) or stable U2OS-HF cells containing an empty vector encoding the same tags. Marais A, Ji Z, Child ES, Krause E, Mann DJ, Sharrocks AD. 2010. Cell cycle-dependent regulation of the Forkhead transcription factor FOXK2 by CDK-cyclin complexes. J Biol Chem. 285: 35728-35739. Anti-Flag (Sigma-Aldrich, F3165)

text: osteosarcoma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex


text: MRC-NIMR

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: mouse embryonic stem cell

text: house mouse

text: Protocols: Mouse ES cells were grown as monolayer in N2B27 medium supplemented with 10ng/ml bFGF (R&D) for 3 days (D1-D3) and then were transferred into serum free media without bFGF (D3-D5).In these conditions cells acquired and anterior neural identity (NA). To induce ventral hindbrain identity NPCs (NH), 100nM RA (Sigma) and 500nM SAG (Calbiochem) was added from D3-D5. Spinal cord identity (NP) was induced by the addition of 5nM CHIR 99021 (Axon) from D2 to D3 followed by 100nM RA, 500nM SAG from D3-D5. To induce mesodermal differentiation the cells were treated with 5uM CHIR99021 from D2-D5 (Meso). RNA samples were collected each day of differentiation from D1 to D5 for the different conditions (NA,NH,NP and Meso). Total RNA was processed according to the TruSeq protocol (Illumina). Three separate read RNA libraries (biological replicates) were barcoded and prepared for each time point. Library size, purity and concentration were determined using Agilent Technologies 2100 Bioanalyzer.

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: frozen specimen

characteristic: specimen with known storage state

characteristic: title


text: Wildtype

characteristic: ArrayExpress-Genotype

text: Lin- bone marrow cells

characteristic: ArrayExpress-OrganismPart

text: wt

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Mus Musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Lin- bone marrow cells

characteristic: sample description

text: Mus musculus


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

tag: Namespace:Medical Research Council, National Institute for Medical Research

text: ArrayExpress

characteristic: broker name

text: chicken

text: Protocols: Intermediate neural plate explants were isolated from HH stage 9 embryos and were cultured in collagen drops (SIGMA) with DMEM for indicated time periods. Chick intermediate neural explants were incubated in the F-12 medium (Gibco) for 0 hour (sample 106) or for 12 hours (samples 107 and 110) in the absence (sample 107) or in the presence of 5nM of bFGF (Fibroblast Growth Factor basic) (sample 110). picopure RNA extraction kit Library was constructed by TruSeq RNA sample preparation kit.

characteristic: description

text: HH stage 9 embryo

characteristic: developmental stage

text: Gallus gallus

characteristic: organism

text: Gallus gallus

text: intermediate region of the neural plate

characteristic: organism part

text: Gallus gallus

text: fresh specimen


text: Medical Research Council, National Institute for Medical Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: chicken

text: HH stage 9 embryo

text: Gallus gallus

text: Gallus gallus

text: intermediate region of the neural plate

text: Gallus gallus

text: fresh specimen

characteristic: specimen with known storage state

characteristic: title


characteristic: ENA-CHECKLIST

text: CDC, U OF S

characteristic: INSDC last update

text: public

characteristic: SRA accession

tag: Namespace:CDC, U OF S

text: TGAC

text: durum wheat

text: Triticum durum cv. strongfield

text: Triticum turgidum subsp. durum

text: Triticum turgidum subsp. durum

text: Wheat CS42 CSS TrDst


text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

characteristic: ArrayExpress-Species

text: SC

text: public

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


text: ESC

characteristic: ArrayExpress-CellType

text: embryonic stem cell line

characteristic: ArrayExpress-DevelopmentalStage

text: AB2.2. Rex1-GFP

characteristic: ArrayExpress-Genotype

characteristic: ArrayExpress-GrowthCondition

text: male

text: Mus musculus

text: AB2.2. Rex1-GFP

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: AB2.2 Rex1-GFP cells. Asynchronous cells stained with 5uM Hoechst staining and sN/Ap frozen on 9/2/2014. RN/A extraction done by Sequencing facility

characteristic: sample description

text: Mus musculus

text: AB2.2. Rex1-GFP

characteristic: strain


text: ESC

text: embryonic stem cell line

text: AB2.2. Rex1-GFP

text: Mus musculus

text: AB2.2. Rex1-GFP

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: AB2.2 Rex1-GFP cells. Cells sorted using 5uM Hoechst staining for G1 phase and sN/Ap frozen on 9/2/2014. RN/A extraction done by Sequencing facility

text: Mus musculus

text: AB2.2. Rex1-GFP


text: ESC

text: embryonic stem cell line

text: AB2.2. Rex1-GFP

text: Mus musculus

characteristic: ArrayExpress-Species

text: AB2.2. Rex1-GFP

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: AB2.2 Rex1-GFP cells. Cells sorted using 5uM Hoechst staining for S phase and sN/Ap frozen on 9/2/2014. RN/A extraction done by Sequencing facility

text: Mus musculus

text: AB2.2. Rex1-GFP


text: ESC

characteristic: ArrayExpress-CellType

text: embryonic stem cell line

characteristic: ArrayExpress-DevelopmentalStage

text: AB2.2. Rex1-GFP

characteristic: ArrayExpress-Genotype

characteristic: ArrayExpress-GrowthCondition

text: Mus musculus

text: AB2.2. Rex1-GFP

text: SC

text: public

text: house mouse

text: Mus musculus

text: AB2.2 Rex1-GFP cells. Cells sorted using 5uM Hoechst staining for G2M phase and sN/Ap frozen on 9/2/2014. RN/A extraction done by Sequencing facility

text: Mus musculus

text: AB2.2. Rex1-GFP


text: Neurons

text: Adult

text: MeCP2 GFP tagged

text: Brain

characteristic: ArrayExpress-OrganismPart

text: wildtype

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

text: Bl6 MeCP2 GFP

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

text: crosslinked and sonicated chromatin= Input from GFP high sample (MeCP2 GFP from 15 BL 6 male)

text: Mus musculus

text: Bl6 MeCP2 GFP


text: Glia

text: Adult

text: MeCP2 GFP tagged

text: Brain

text: wildtype

text: male

text: Mus musculus

text: Bl6 MeCP2 GFP

characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: crosslinked and sonicated chromatin= Input from GFP low sample (MeCP2 GFP from 15 BL 6 male)

characteristic: sample description

text: Mus musculus

text: Bl6 MeCP2 GFP

characteristic: strain


text: Liver

characteristic: ArrayExpress-CellType

text: Adult

characteristic: ArrayExpress-DevelopmentalStage

text: MeCP2 GFP tagged

text: Liver

text: wildtype

text: male

text: Mus musculus

characteristic: ArrayExpress-Species

text: Bl6 MeCP2 GFP

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: crosslinked and sonicated chromatin= Input from Liver (MeCP2 GFP from 15 BL 6 male)

text: Mus musculus

text: Bl6 MeCP2 GFP


text: Kidney

text: Embryonic

text: wildtype

characteristic: ArrayExpress-Genotype

text: Kidney

characteristic: ArrayExpress-OrganismPart

text: wildtype

characteristic: ArrayExpress-Phenotype

text: female

characteristic: ArrayExpress-Sex

text: Homo Sapiens

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: human

text: Homo sapiens

text: crosslinked and sonicated chromatin= Input from Hek293FT cells

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, United Kingdom

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human osteosarcoma cell

characteristic: cell type

text: human

text: Protocols: Human osteosarcoma (U2OS) cells were obtained from CRUK and grown at 37C according to standard cell culture protocols. U2OS cells were grown at 37C and either left untreated or incubated at 43C for 30 minutes to induce heat shock. Approximately 3.5-4.5 x 10 ^ 7 U2OS cells were used per treatment. Cells were chemically cross-linked by adding formaldehyde solution directly into cell culture medium to a final concentration of 1 %. Cells were fixed by incubation at room temperature for 10 min, followed by incubation with 0.125 M glycine for 5 min. Cells were washed twice and scraped into ice-cold PBS. Cell pellets were flash frozen in liquid nitrogen and stored at -80C. Frozen cell pellets were lysed in 2.1 ml lysis buffer containing 1% SDS, 10 mM EDTA, 50 mM Tris (pH 8.1), and protease inhibitors. To shear chromatin to fragments of about 200-500 bp size, samples were sonicated in 300 _l volumes for 14 cycles (7.5 min total sonication time) at high setting using a Bioruptor (Diagenode). Sonicated lysates were then cleared by centrifugation for 10 min at high speed, diluted 1/10 with dilution buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris at pH 8.1) and incubated with SUMO-2 antibody (Life Technologies, 51-9100) and 0.1% Brij-35 overnight at 4C. In detail, to capture protein-DNA complexes, a fraction corresponding to 90% of the lysate volume was incubated with 21 ug SUMO-2 antibody and subsequently with protein G sepharose 4B beads (Sigma) for 1 h using a final bead bed volume of 150 ul. To reduce non-specific binding, beads had been pre-incubated with 0.5% (w/v) BSA in PBS overnight. Libraries were constructed using approximately 10 ng purified DNA. Single-end libraries were generated using either the Illumina ChIP-seq DNA sample Preparation Kit (IP-102-1001) or the TruSeq DNA sample preparation kit (PE-940-2002). In brief, ChIP or input DNA was end repaired and A-tailed before adaptors were ligated on the fragments. The ligated samples were then size selected on a 2 % low melting agarose gel to approximately 250-300 bp. An 18 cycle PCR was performed and libraries were quantified using a Nanodrop Spectrophotometer. Library quality was validated by High Sensitivity Bioanalyzer ChIP (Agilent).

characteristic: description

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex

text: fresh specimen

characteristic: specimen with known storage state

characteristic: title


text: Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, United Kingdom

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human osteosarcoma cell

text: human

characteristic: common name

text: Protocols: Human osteosarcoma (U2OS) cells were obtained from CRUK and grown at 37C according to standard cell culture protocols. U2OS cells were grown at 37C and either left untreated or incubated at 43C for 30 minutes to induce heat shock. Bead-bound protein-DNA complexes were washed twice in approximately 14 ml of each wash buffer I (0.1% SDS, 1% Triton X-100, 2 mM EDTA pH 8.0, 20 mM Tris pH 8.1, 150 mM NaCl), wash buffer II (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA pH 8.0, 20 mM Tris pH 8.1, 500 mM NaCl) wash buffer III (0.25 mM LiCl, 1 % NP-40, 1 % sodium deoxycholate, 1 mM EDTA pH 8.0, 10 mM Tris pH 8.1) and TE buffer (10 mM Tris pH 8.1, 1 mM EDTA pH 8.0) and eluted into 2.5 ml elution buffer containing 1% SDS and 0.1 M sodium bicarbonate for 20 min at 30C while shaking. An equal volume of TE buffer was added to eluates prior to digestion of RNA by incubation with 0.2 mg/ml RNase A (Fermentas) at 37C for 2 hours. Reversal of cross-links was carried out by incubation in the presence of 0.2 M sodium chloride overnight at 65C, followed by incubation with 0.25 mg/mL proteinase K (Roche), 40 mM Tris pH 6.5 and 10 mM EDTA for 1 h at 55C. DNA was purified using a PCR purification kit (Qiagen). To derive genomic DNA to be used as an input reference for SUMO-2 ChIP-seq, a fraction corresponding to the sonicated, diluted and cleared whole cell extracts that had been prepared for SUMO-2 ChIP was removed. These input samples were treated for removal of RNA and cross-link reversal and DNA was extracted as described above. Approximately 3.5-4.5 x 10^7 U2OS cells were used per treatment. Cells were chemically cross-linked by adding formaldehyde solution directly into cell culture medium to a final concentration of 1 %. Cells were fixed by incubation at room temperature for 10 min, followed by incubation with 0.125 M glycine for 5 min. Cells were washed twice and scraped into ice-cold PBS. Cell pellets were flash frozen in liquid nitrogen and stored at -80C. Frozen cell pellets were lysed in 1.8 ml lysis buffer containing 1% SDS, 10 mM EDTA, 50 mM Tris (pH 8.1), and protease inhibitors. To shear chromatin to fragments of about 200-500 bp size, samples were sonicated in 300 _l volumes for 15 cycles (7.5 min total sonication time) at high setting using a Bioruptor (Diagenode). Sonicated lysates were then cleared by centrifugation for 10 min at high speed, diluted 1/10 with dilution buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris at pH 8.1) and incubated with SUMO-2 antibody (Life Technologies, 51-9100) and 0.1% Brij-35 overnight at 4C. In detail, to capture protein-DNA complexes, lysates were incubated with 13 ug SUMO-2 antibody and subsequently with protein G Dynabeads (Life Technologies) for 1 h using an equivalent of 300 ul bead solution. To reduce non-specific binding, beads had been pre-incubated with 0.5% (w/v) BSA in PBS overnight. Bead-bound protein-DNA complexes were washed twice in approximately 13 ml of each wash buffer I (0.1% SDS, 1% Triton X-100, 2 mM EDTA pH 8.0, 20 mM Tris pH 8.1, 150 mM NaCl), wash buffer II (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA pH 8.0, 20 mM Tris pH 8.1, 500 mM NaCl) wash buffer III (0.25 mM LiCl, 1 % NP-40, 1 % sodium deoxycholate, 1 mM EDTA pH 8.0, 10 mM Tris pH 8.1) and TE buffer (10 mM Tris pH 8.1, 1 mM EDTA pH 8.0) and eluted into 2.3 ml elution buffer containing 1% SDS and 0.1 M sodium bicarbonate for 20 min at 30C while shaking. An equal volume of TE buffer was added to eluates prior to digestion of RNA by incubation with 0.2 mg/ml RNase A (Fermentas) at 37C for 2 hours. Reversal of cross-links was carried out by incubation in the presence of 0.2 M sodium chloride overnight at 65C, followed by incubation with 0.25 mg/mL proteinase K (Roche), 40 mM Tris pH 6.5 and 10 mM EDTA for 1 h at 55C. DNA was purified using a PCR purification kit (Qiagen). Libraries were constructed using approximately 10 ng purified DNA. Single-end libraries were generated using either the Illumina ChIP-seq DNA sample Preparation Kit (IP-102-1001) or the TruSeq DNA sample preparation kit (PE-940-2002). In brief, ChIP or input DNA was end repaired and A-tailed before adaptors were ligated on the fragments. The ligated samples were then size selected on a 2 % low melting agarose gel to approximately 250-300 bp. An 18 cycle PCR was performed and libraries were quantified using a Nanodrop Spectrophotometer. Library quality was validated by High Sensitivity Bioanalyzer ChIP (Agilent).

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: female

text: fresh specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: human osteosarcoma cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

text: fresh specimen


text: Mouse

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: UWEST

text: public

text: Platinum_PCR_SuperMix_High_Fidelity_(Invitrogen)

text: TCCTTGATGTTC

characteristic: barcode sequence

characteristic: collection site

text: house mouse

text: Sequencing_of_bacterial_16S_rRNA_gene_from_mouse_brain.

characteristic: description

characteristic: extraction

text: PureLink_Genomic_DNA_Mini_Kit_(Invitrogen)_(modified_protocol)

characteristic: nucleic acid extraction

text: Mus musculus

characteristic: pcr conditions

text: forward_primer:_S-D-Bact-0341-b-S-17,_5'-CCTACGGGNGGCWGCAG-3',_reverse_primer:_S-D-Bact-0515-a-A-19,_5'-TTACCGCGGCTGCTGGCAC-3'

characteristic: pcr primers

text: R_2012_05_21_03_54_52_user_SN1-31-Animal_Brain_Bugs

characteristic: run id

text: Mus musculus

text: brain

characteristic: tissue site

text: Mouse Olfactory bulb 16S V3 amplicon


text: UWEST

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: TCTAGCTCTTC

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus

text: brain

text: Mouse Olfactory bulb 16S V3 amplicon

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UWEST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: TCACTCGGATC

text: house mouse

text: Mus musculus

text: Mus musculus

text: brain

text: Mouse Olfactory bulb 16S V3 amplicon


text: UWEST

text: public

text: CCGCATGGAAC

characteristic: barcode sequence

characteristic: collection site

text: house mouse

text: Sequencing_of_bacterial_16S_rRNA_gene_from_mouse_nasal_washes.

characteristic: description

characteristic: extraction

characteristic: nucleic acid extraction

text: Mus musculus

characteristic: pcr conditions

text: Mus musculus

text: Mouse nasal wash 16S V3 amplicon


text: UWEST

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CTGGCAATCCTC

text: house mouse

text: Mus musculus

characteristic: pcr primers

characteristic: run id

text: Mus musculus

characteristic: tissue site

text: Mouse nasal wash 16S V3 amplicon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UWEST

text: public

characteristic: Submitter Id

text: CCGGAGAATCGC

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mouse nasal wash 16S V3 amplicon

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UWEST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: TTCCTGCTTCAC

characteristic: barcode sequence

characteristic: collection site

text: Norway rat

text: Sequencing_of_bacterial_16S_rRNA_gene_from_rat_brain.

text: Rattus norvegicus

text: Rattus norvegicus

text: brain

text: Rat olfactory bulb 16S V3 amplicon


text: UWEST

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CCTTAGAGTTC

text: Norway rat

characteristic: description

characteristic: extraction

characteristic: nucleic acid extraction

text: Rattus norvegicus

characteristic: pcr conditions

text: Rattus norvegicus

text: brain

text: Rat olfactory bulb 16S V3 amplicon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UWEST

text: public

characteristic: SRA accession

text: CTGAGTTCCGAC

text: Norway rat

text: Rattus norvegicus

characteristic: pcr primers

characteristic: run id

text: Rattus norvegicus

text: brain

characteristic: tissue site

text: Rat olfactory bulb 16S V3 amplicon


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UWEST

text: public

characteristic: Submitter Id

text: TCCACCTCCTC

text: Norway rat

characteristic: common name

text: Sequencing_of_bacterial_16S_rRNA_gene_from_rat_nasal_washes.

text: Rattus norvegicus

characteristic: organism

text: Rattus norvegicus

text: Rat nasal wash 16S V3 amplicon

characteristic: title


text: UWEST

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CAGCATTAATTC

characteristic: barcode sequence

characteristic: collection site

text: Norway rat

text: Rattus norvegicus

text: Rattus norvegicus

text: Rat nasal wash 16S V3 amplicon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UWEST

text: public

text: TCTGGCAACGGC

text: Norway rat

characteristic: description

characteristic: extraction

characteristic: nucleic acid extraction

text: Rattus norvegicus

characteristic: pcr conditions

text: Rattus norvegicus

text: Rat nasal wash 16S V3 amplicon


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UWEST

text: public

characteristic: SRA accession

text: CGAAGGCCACAC

text: human

text: Sequencing_of_bacterial_16S_rRNA_gene_from_human_brain

text: Homo sapiens

characteristic: pcr primers

characteristic: run id

text: Homo sapiens

characteristic: tissue site

text: Human olfactory bulb 16S V3 amplicon


text: UWEST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: TCTGCCTGTC

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Human olfactory bulb 16S V3 amplicon

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UWEST

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CGATCGGTTC

characteristic: barcode sequence

characteristic: collection site

text: human

text: Homo sapiens

text: Homo sapiens

text: Human olfactory bulb 16S V3 amplicon


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UWEST

text: public

text: TCAGGAATAC

text: human

text: Control_(nature_of_control_not_disclosed)

characteristic: description

characteristic: extraction

characteristic: nucleic acid extraction

text: Homo sapiens

characteristic: pcr conditions

text: Homo sapiens

text: Control


text: UWEST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: CGGAAGAACCTC

text: human

text: Sequencing_of_bacterial_16S_rRNA_gene_from_human_nasal_wash

text: Homo sapiens

characteristic: pcr primers

characteristic: run id

text: Homo sapiens

characteristic: tissue site

text: Human nasal wash 16S V3 amplicon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UWEST

text: public

characteristic: Submitter Id

text: CGAAGCGATTC

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Human nasal wash 16S V3 amplicon

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UWEST

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CAGCCAATTCTC

characteristic: barcode sequence

characteristic: collection site

text: human

text: Homo sapiens

text: Homo sapiens

text: Human nasal wash 16S V3 amplicon


text: UWEST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: CCTGGTTGTC

text: human

characteristic: description

characteristic: extraction

characteristic: nucleic acid extraction

text: Homo sapiens

characteristic: pcr conditions

text: Homo sapiens

text: Control


text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: SRA accession

text: human

text: Homo sapiens

text: Homo sapiens


text: female

text: Homo Sapien

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens


characteristic: External Id

text: DUNDEE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: fruit fly

text: Protocols: Cells were cultured in the presence of 10% FBS in DMEM (U2OS cells) or in Schneider's medium (Kc167 cells). Both cell types were stimulated with 10 % extra FBS for 1h followed by 250 uM cycloheximide for 10 min. Cells were rinsed twice with cold PBS and lysed in 1 ml polysome extraction buffer (1 % deoxycholate, 1 % NP40, 10 mM HEPES (pH 7.4), 350 mM KCl, 5 mM MgCl2, 5 mM CaCl2, 250 uM cycloheximide, 1x protease inhibitors (Sigma, P8340) and 2 ul RiboLock RNase inhibitor (ThermoFisher). Lysates were centrifuged for 10 min at 16000 xg and supernatant (leaving lowest ~25% behind) was used for ribosome profiling.The lysate samples were split in to two different digestion samples and digested with either 200 U of E. coli MBP-RNAse I (New England BioLabs) or 100 U of MN (ThermoFisher) by incubating for 40 min (U2OS) or 60 min (Kc167) at RT with slow mixing. 2 U of DNase I (ThermoFisher) was also added to each U2OS sample at the start of digestion. MN reaction was stopped with 10 mM EGTA. The samples were centrifuged at 6000 xg for 5 min to pellet insoluble material. The ribosomes were separated by sucrose step centrifugation using 0.5 M sucrose in polysome extraction buffer supplied with SUPERase-In (1/500) (Ambion). 0.35 ml lysate was layered on top of 0.2 ml sucrose cushion and centrifuged at 100000 xg for 45 min (55000 rpm using TLA 120.1 rotor). Supernatant was removed and pellet was suspended in 600 ul Qiazol reagent (Qiagen). Samples were incubated for 15 min at 70C with mixing to dissolve the pellet after which 200 ul of chloroform was added, the samples were vortexed and centrifuged for 10 min at 12000 xg at 4C. RNA was precipitated in the presence of Pink Co-precipitant (Bioline) at -80C o/n. RNA was washed and suspended in 20 ul of sterile water and mixed with 80 ul 2x TBE-urea sample buffer (without Xylene Cyanol FF). Samples were run on a 15 % TBE-urea gel, the gel was stained using 1x SYBR Gold (Invitrogen) and 28-35 nt sized RNA was cut out of the gel with the help of oligoribonucleotide size markers (28 and 35 nt RNA oligos). The gel pieces were disrupted and RNA was eluted with 300 mM NaAcetate (pH 5.0), 1 mM EDTA and SUPERase-In for 30 min at 65C. RNA was precipitated, centrifuged and washed with 80% ethanol and then suspended in 5 ul of sterile water. RNA yields were quantified with SYBR Gold using Qubit fluorometer (Invitrogen). All samples had over 1 pmol/ul RNA. 5-15 picomoles of each RNA sample was used for phosphatase and poly-A tailing reaction by mixing 3.25 ul of RNA with the following: 0.5 ul 10x poly-A buffer (0.5 M Tris-HCl, pH 7.0, 2.5 M NaCl, 100 mM MgCl2, 50 mM DTT, 1 mg/ml BSA), 0.25 ul Yeast poly-A polymerase (600 U/ul, Affymetrix), 0.5 ul 10 mM ATP, 0.3 ul (3 U) T4 polynucleotide kinase (ThermoFisher), 0.2 ul SUPERase-In. Samples were incubated at 37C for 3 h. Note that RNase I digestion results in cyclic 2'3'-phosphate, which will be resolved by the inherent phosphatase activity of the T4 polynucleotide kinase. 4 ul of each sample was mixed with 1 ul 10 uM abasic-oligo dT primers containing random 8 nt sequence used for absolute molecular counting (Casbon et al., 2011; Kivioja et al., 2012), incubated at 72C for 3 min and put on ice. Reverse transcription was started by adding the following to the samples: 5.25 ul H20, 3 ul 5x RT-buffer (ThermoFisher), 0.75 ul 10 mM dNTP, 0.25 ul SUPERase-In and 0.4 ul Maxima Reverse transcriptase (75 U, ThermoFisher). Samples were incubated at 50C for 1 h, heat inactivated at 85C for 6 min after which 0.5 ul RNAse H (ThermoFisher) was added and samples were incubated at 37C for 30 min. Reverse transcription products were purified on 10% TBE-urea gel and cDNA was eluted into 700 ul of DNA gel elution buffer (1x TE + 300 mM NaCl) by incubating o/n at 4C with mixing on Eppendorf Thermomixer. cDNA was precipitated as before, samples were centrifuged for 10 min at 16000 g, pellets were washed and cDNA was suspended into 5 ul of circularization mix (0.5 ul CircLigase buffer (10x), 0.25 ul 50 mM MnCl2, 0.25 ul CircLigase II (Epicentre), 1 ul 5 M betaine, 3 ul sterile water). Samples were incubated o/n at 60C and heat-inactivate for 10 min at 80C. cDNA was linearized by adding 3 ul of relinearization supplement (50 mM KCl, 1 mM DTT) followed by 0.7 ul (7 U) APE1 (New England Biolabs). Samples were incubated for 1 hour at 37C. Libraries were then amplified using 18 cycles of PCR with Solexa-primer-F and R and Phusion DNA polymerase (ThermoFisher). PCR products were separated on agarose gel, eluated using Qiagen MinElute Gel extraction kit and quantified with Quant-it PicoGreen DNA dye (LifeTechnologies) using Qubit fluorometer (LifeTechnologies).

text: wild type genotype

characteristic: genotype

text: Drosophila melanogaster

text: Drosophila melanogaster

text: Drosophila melanogaster

text: female

characteristic: sex

text: fresh specimen

characteristic: specimen with known storage state

characteristic: title


text: DUNDEE

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: human

characteristic: description

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

text: fresh specimen


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: LRI CRUK

text: public

characteristic: SRA accession

tag: Namespace:LRI CRUK

text: ArrayExpress

text: embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: Fetal livers were dissected from embryos at day 14.5 (E14.5) of development. Fetal liver cells were filtered through a cell strainer (70uM) and directly fixed in formaldehyde. Hi-C was performed following (Lieberman-Aiden et al., Science, 2009, DOI: 10.1126/science.1181369 ) with modifications detailed in Schoenfelder et al.). For CHiC experiments promoter interactions were enriched using a biotynilated RNA bait library as described. For random ligation (RL) libraries the crosslink was reversed before the ligation step in the HiC protocol, the dilution step was omitted, and the library was enriched the same way as described for CHiC.

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: LRI CRUK

text: public

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: common name

text: embryonic day 14.5

characteristic: developmental stage

text: Mus musculus

characteristic: organism

text: Mus musculus

text: fetal liver

characteristic: organism part

text: Mus musculus


characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:School of Agriculture, Policy and Development, The University of Reading, UK

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Immature zygotic embryos collected after 5 d of inoculation on B5 medium supplemented with 5 uM 2, 4-dichlorophenoxyacetic acid Protocols: Somatic embryos were induced on B5 medium supplemented with 5 uM 2, 4-dichlorophenoxyacetic acid (Gaj, 2001). In vitro cultures were maintained at 24C under a 16 h/ 8 h (light/dark) cycle in a culture room. Samples were collected after 5 d of in vitro culture. Approximately 700 embryogenic cultures induced at each time-point were pooled together to extract total RNA. Total RNA was extracted using the RNeasy® Plant Mini Kit (Qiagen, UK) according to the manufacturers protocol. The cDNA libraries were constructed in accordance with the Illumina TruSeq RNA sample preparation guide v2 for Illumina paired-end multiplexed sequencing.

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: somatic embryo

text: Arabidopsis thaliana

text: frozen specimen

characteristic: specimen with known storage state


text: School of Agriculture, Policy and Development, The University of Reading, UK

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: thale cress

text: Immature zygotic embryos collected after 15 d of inoculation on B5 medium supplemented with 5 uM 2, 4-dichlorophenoxyacetic acid Protocols: Somatic embryos were induced on B5 medium supplemented with 5 uM 2, 4-dichlorophenoxyacetic acid (Gaj, 2001). In vitro cultures were maintained at 24C under a 16 h/ 8 h (light/dark) cycle in a culture room. Samples were collected after 15 d of in vitro culture. Approximately 700 embryogenic cultures induced at each time-point were pooled together to extract total RNA. Total RNA was extracted using the RNeasy® Plant Mini Kit (Qiagen, UK) according to the manufacturers protocol. The cDNA libraries were constructed in accordance with the Illumina TruSeq RNA sample preparation guide v2 for Illumina paired-end multiplexed sequencing.

characteristic: description

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: somatic embryo

text: Arabidopsis thaliana

text: frozen specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: ArrayExpress

text: thale cress

text: Immature zygotic embryos collected after 10 d of inoculation on B5 medium supplemented with 5 uM 2, 4-dichlorophenoxyacetic acid Protocols: Somatic embryos were induced on B5 medium supplemented with 5 uM 2, 4-dichlorophenoxyacetic acid (Gaj, 2001). In vitro cultures were maintained at 24C under a 16 h/ 8 h (light/dark) cycle in a culture room. Samples were collected after 10 d of in vitro culture. Approximately 700 embryogenic cultures induced at each time-point were pooled together to extract total RNA. Total RNA was extracted using the RNeasy® Plant Mini Kit (Qiagen, UK) according to the manufacturers protocol. The cDNA libraries were constructed in accordance with the Illumina TruSeq RNA sample preparation guide v2 for Illumina paired-end multiplexed sequencing.

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: somatic embryo

text: Arabidopsis thaliana

text: frozen specimen


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WTCHG

text: public

text: ArrayExpress

text: human

text: Protocols: Blood from Leukocyte Cone was processed using a Ficoll separation method [Neron S, Thibault L, Dussault N, Cote G, Ducas E, Pineault N, Roy A. 2007. Characterization of mononuclear cells remaining in the leukoreduction system chambers of apheresis instruments after routine platelet collection: a new source of viable human blood cells. Transfusion 47(6): 1042-1049 ]. Buffy coat was isolated and washed in HBSS buffer. Buffy coat was subjected to purification via positive selection with CD19-coated beads (Miltenyi AUTOMACS) following manufacturers procedures. 20-40 million cells were crosslinked and immunoprecipitated as per procedure described within manuscript in preparation. Following manufacturers recommended procedures

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: fresh specimen


text: WTCHG

text: public

text: E-MTAB-2424:Monocyte_treated_indiv1_RFX5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: Blood from Leukocyte Cone was processed using a Ficoll separation method [Neron S, Thibault L, Dussault N, Cote G, Ducas E, Pineault N, Roy A. 2007. Characterization of mononuclear cells remaining in the leukoreduction system chambers of apheresis instruments after routine platelet collection: a new source of viable human blood cells. Transfusion 47(6): 1042-1049 ]. Buffy coat was isolated and washed in HBSS buffer. CD19-depleted flow-through was subjected to purification via positive selection with CD14-coated beads (Miltenyi AUTOMACS) following manufacturers procedures. Purified, naive monocytes (CD14 + selected) were incubated for 24 hours in RPMI supplemented with 2mM Glutamine (Sigma), 100U/ml penicillin (Sigma), 0.1mg/ml streptomycin (Sigma) and 20% FCS (Sigma) at 37C in 5% CO2. Treated cells were incubated alongside a naive control but with the addition of interferon-gamma (R&D Systems) to final concentration of 10 ng/mL. 20-40 million cells were crosslinked and immunoprecipitated as per procedure described within manuscript in preparation. Following manufacturers recommended procedures

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: fresh specimen


text: WTCHG

text: public

text: ArrayExpress

text: human

text: Protocols: Blood from Leukocyte Cone was processed using a Ficoll separation method [Neron S, Thibault L, Dussault N, Cote G, Ducas E, Pineault N, Roy A. 2007. Characterization of mononuclear cells remaining in the leukoreduction system chambers of apheresis instruments after routine platelet collection: a new source of viable human blood cells. Transfusion 47(6): 1042-1049 ]. Buffy coat was isolated and washed in HBSS buffer. Buffy coat was subjected to purification via positive selection with CD19-coated beads (Miltenyi AUTOMACS) following manufacturers procedures. Crosslinked chromatin was purified for use as an estimate of background. Following manufacturers recommended procedures

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: fresh specimen


text: WTCHG

text: public

text: ArrayExpress

text: human

text: Protocols: Blood from Leukocyte Cone was processed using a Ficoll separation method [Neron S, Thibault L, Dussault N, Cote G, Ducas E, Pineault N, Roy A. 2007. Characterization of mononuclear cells remaining in the leukoreduction system chambers of apheresis instruments after routine platelet collection: a new source of viable human blood cells. Transfusion 47(6): 1042-1049 ]. Buffy coat was isolated and washed in HBSS buffer. CD19-depleted flow-through was subjected to purification via positive selection with CD14-coated beads (Miltenyi AUTOMACS) following manufacturers procedures. Crosslinked chromatin was purified for use as an estimate of background. Following manufacturers recommended procedures

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: fresh specimen


text: WTCHG

characteristic: INSDC last update

text: public

text: E-MTAB-2424:Monocyte_treated_indiv2_CIITA

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: fresh specimen


text: WTCHG

text: public

characteristic: INSDC status

text: ArrayExpress

text: human

text: Protocols: Blood from Leukocyte Cone was processed using a Ficoll separation method [Neron S, Thibault L, Dussault N, Cote G, Ducas E, Pineault N, Roy A. 2007. Characterization of mononuclear cells remaining in the leukoreduction system chambers of apheresis instruments after routine platelet collection: a new source of viable human blood cells. Transfusion 47(6): 1042-1049 ]. Buffy coat was isolated and washed in HBSS buffer. CD19-depleted flow-through was subjected to purification via positive selection with CD14-coated beads (Miltenyi AUTOMACS) following manufacturers procedures. 20-40 million cells were crosslinked and immunoprecipitated as per procedure described within manuscript in preparation. Following manufacturers recommended procedures

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: fresh specimen


text: WTCHG

text: public

text: E-MTAB-2424:Monocyte_treated_indiv1_CIITA

text: ArrayExpress

characteristic: broker name

text: human

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: fresh specimen


text: WTCHG

text: public

text: E-MTAB-2424:Monocyte_treated_indiv2_RFX5

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: fresh specimen

characteristic: specimen with known storage state


text: CIPF

characteristic: INSDC center name

text: public

text: calamondin

text: Citrus x microcarpa

text: Citrus x microcarpa

text: Citrus madurensis


text: Endocrine cancer staff scientist

characteristic: INSDC first public

text: public

tag: Namespace:Endocrine cancer staff scientist

text: ArrayExpress

text: human

text: Protocols: DNA was extracted from frozen tumor using standard methods Whole exome enrichment was performed according to Agilent's Sureselect Human All Exon Kit protocol

text: multiple paraganglioma

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: male

characteristic: sex

text: frozen specimen

text: dead

characteristic: viability


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, United Kingdom

text: public

text: ArrayExpress

characteristic: cell line

text: human osteosarcoma cell

characteristic: cell type

text: human

text: Protocols: Human osteosarcoma (U2OS) cells were obtained from CRUK and grown at 37C according to standard cell culture protocols. U2OS cells were grown at 37C and either left untreated or incubated at 43C for 4 hours to induce heat shock. Qiagen RNeasy mini kit according to manufacturer's instructions including DNAseI digestion step Isolated total RNA was incubated with DNaseI to digest residual genomic DNA. Poly-A mRNA was purified from the total RNA sample using oligo(dT) coated magnetic beads and eluted with Tris-HCl and heating. Isolated mRNA was fragmented and used for reverse transcription of cDNA (first and second strand cDNA synthesis). Purified cDNA was subjected to end-repair and A-tailing followed by adaptor ligation. Adaptor-ligated cDNA fragments were then PCR amplified and quality and quantity of the cDNA library was validated on an Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-time PCR system, respectively.

characteristic: description

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

text: fresh specimen

characteristic: title


characteristic: ArrayExpress-Genotype

text: VNO

characteristic: ArrayExpress-OrganismPart

text: Wildtype

characteristic: ArrayExpress-Phenotype

text: female

characteristic: ArrayExpress-Sex

text: Mouse

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: RNA from VNO

characteristic: sample description

text: Mus musculus

characteristic: strain


text: MOE

text: Wildtype

text: male

text: Mouse

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: RNA from MOE

text: Mus musculus


characteristic: ArrayExpress-Genotype

text: MOE

characteristic: ArrayExpress-OrganismPart

text: Wildtype

characteristic: ArrayExpress-Phenotype

text: female

characteristic: ArrayExpress-Sex

text: Mouse

text: SC

text: public

text: house mouse

text: Mus musculus

text: RNA from MOE

text: Mus musculus


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: UPSC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: thale cress

characteristic: common name

text: pool of homozygous young seedlings at the rosette stage

characteristic: description

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana re-sequencing project

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UPSC

text: public

text: thale cress

text: pool of homozygous young seedlings at the rosette stage F3 generation after the 4th backcross

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana


text: UPSC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: thale cress

text: pool of homozygous young seedlings at the rosette stage F3 generation after the 2nd backcross

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: Universite Joseph Fourier Grenoble

text: public

characteristic: INSDC status

tag: Namespace:Universite Joseph Fourier Grenoble

text: 5 month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: western clawed frog

text: Protocols: Xenopus (X. tropicalis) females were purchased from the Xenopus national husbandry (CRB Xenopes), University of Rennes 1 (http://xenopus.univ-rennes1.fr/). The frogs were fed daily ad libitum with pellets of trout food. They were allowed to acclimatize for 3 weeks at 25ﾰC with a photoperiod of 12h:12h in constantly filtered water prior to starting the experiments Xenopus were exposed individually at 25ﾰC in 1 L glass jars protected from the light (3 individual replicates by times and exposure conditions). The exposure solutions consisted of 500 mL tap water (pH 7.8, organic carbon = 0.6 mg L-1, dissolved oxygen = 9.9 mg L-1, nitrate = 2.9 mg L-1, nitrites < 0.02 mg L-1) containing BaP at an initial concentration of 10 ﾵg L-1. Control frogs were exposed to ethanol (vehicle) at 1/1000 (v:v) concentration. To avoid circadian effects, experiments with control and BaP-exposed animals were conducted in parallel. The frogs were not fed during the exposure period (from 0 to 24h) For each biological replicate, total RNA was extracted from 15 mg liver using the RNAqueousﾮ-4PCR Kit (Ambion, USA) according to manufacturer's instructions. Total RNA quality and quantity were controlled on an Agilent 2100 Bioanalyzer (Agilent, USA). After extraction, total RNA from each biological replicate were equally pooled in order to obtain 8ﾵg of total RNA in 50ﾵl for each treatment and used for mRNAseq banks preparations using mRNA-Seq-8 Sample Prep Kit (Illumina, USA) according to manufacturer's instructions.

text: adults

characteristic: developmental stage

text: Xenopus (Silurana) tropicalis

text: Xenopus tropicalis

text: liver

characteristic: organism part

text: Xenopus (Silurana) tropicalis

text: female

characteristic: sex

characteristic: specimen with known storage state


text: cultured human neurons

characteristic: ArrayExpress-CellType

text: MeCP2 shRNA 2

characteristic: ArrayExpress-Genotype

text: Brain

characteristic: ArrayExpress-OrganismPart

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

characteristic: ArrayExpress-Species

text: day 9

characteristic: ArrayExpress-TimePoint

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Total cDNA from human neurons

characteristic: sample description

text: Homo sapiens


text: cultured human neurons

text: MeCP2 shRNA 3

text: Brain

text: female

text: Homo sapiens

text: day 9

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Total cDNA from human neurons

text: Homo sapiens


text: cultured human neurons

characteristic: ArrayExpress-CellType

text: scrambled control

characteristic: ArrayExpress-Genotype

text: Brain

characteristic: ArrayExpress-OrganismPart

text: female

text: Homo sapiens

text: day 9

text: SC

text: public

text: human

text: Homo sapiens

text: Total cDNA from human neurons

text: Homo sapiens


text: cultured human neurons

text: MeCP2 overexpression

text: Brain

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

characteristic: ArrayExpress-Species

text: day 9

characteristic: ArrayExpress-TimePoint

text: SC

text: public

text: human

text: Homo sapiens

text: Total cDNA from human neurons

text: Homo sapiens


text: cultured human neurons

text: control overexpression

text: Brain

text: female

text: Homo sapiens

text: day 9

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

text: human

text: Homo sapiens

text: Total cDNA from human neurons

text: Homo sapiens


text: cultured human neurons

text: control non-infected

text: Brain

text: female

text: Homo sapiens

text: day 9

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Total cDNA from human neurons

characteristic: sample description

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

text: NCGR

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: grass carp

text: Grass carp female individual

characteristic: description

text: Ctenopharyngodon idella

text: Ctenopharyngodon idella

text: Grass carp accession (Ctenopharyngodon idellus) GCF01

characteristic: title


text: NCGR

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: grass carp

characteristic: common name

text: Grass carp male individual

text: Ctenopharyngodon idella

characteristic: organism

text: Ctenopharyngodon idella

text: Grass carp accession (Ctenopharyngodon idellus) GCM01


status: KILLED

characteristic: ArrayExpress-Phenotype

text: male

characteristic: ArrayExpress-Sex

text: Homo Sapien

characteristic: ArrayExpress-Species

text: SC

text: killed

characteristic: Sample Description

characteristic: Strain

text: human

text: Homo sapiens

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NCGR

text: public

characteristic: SRA accession

text: grass carp

text: RNA sequencing of grass carp

text: Ctenopharyngodon idella

text: Ctenopharyngodon idella

text: Grass carp (Ctenopharyngodon idellus) transcriptome


characteristic: ENA-FIRST-PUBLIC

text: NCGR

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: grass carp

text: Whole genome bisulfite sequencing of the grass carp

text: Ctenopharyngodon idella

text: Ctenopharyngodon idella

text: Grass carp (Ctenopharyngodon idellus) epigenome


text: EMBL European Bioinformatics Institute

characteristic: INSDC first public

text: public

tag: Namespace:EMBL European Bioinformatics Institute

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: Protocols: Wt yeast (BY4741, which is derived from S288c) and delta-ccr4/pan2 (Beilharz et al., RNA. 2007 Jul;13(7):982-97) were single colony streaked on YPAD-agar plates, and then 2 individual colonies each were inoculated in 2ml YPAD medium and grown o.n. at 30C at 180rpm. OD was measured and 7x107 cells were pelleted, resuspended in 2ml Y1 medium (2ul beta-ME, 150ul zymolase) and incubated for 30min at 30C in a waterbath. After centrifugation, the pellet was lysed in buffer RLT and processed according to the yeast protocol of the Qiagen RNeasy kit. Yield and quality of totalRNA was measured with Nanodrop and confirmed by Agilent RNA Nano chip (RIN 10). A DNase digestion was performed on 20ug totalRNA using Turbo DNase (Life Technologies), followed by an RNeasy column cleanup step and elution into 30ul nuclease free water (Ambion). Poly(A) selection: 2 rounds of polyA selection were performed using the Truseq RNA Sample Preparation kit (Illumina) with several modifications. In more detail: 50ul of DNase digested totalRNA was incubated with 50ul RNA Purification beads (oligo-dT) for 5min at 65C, cooled to 4C, and then incubated for 5min at RT in a DNA Engine tetrade 2 (Biorad) thermocycler. Afterwards, beads were separated with a magnet and washed with 200ul Bead Wash buffer, and then eluted in 50ul elution buffer for 2min at 80C. On RT, 50ul of binding buffer were added, placed on a magnet and washed with 200ul Bead Wash buffer, and again eluted in 50ul elution buffer for 2min at 80C. The supernatant containing the mRNA was transferred into a 1.5ml Low Binding tube (Eppendorf) and quantified with the Qubit RNA assay. Spike-in control: 20ul of spike in in vitro transcripts with a known A42 stretch (Pelechano V. et al., Nature. 2013 May 2;497(7447):127-31) were added. A cleanup step was performed using the RNeasy MinElute Cleanup Kit (Qiagen) according to protocol eluting with 14ul water. G-tailing and fragmentation: The USB Poly(A) Tail-Length Assay kit (Affymetrix) was used with several modifications to add a short G stretch to the 3’end of the mRNA. In detail, 14ul mRNA (with spike-in) were incubated with 4ul of 5xTail buffer mix and 2ul 10x Tail Enzyme mix at 37C for 1h and stopped by addition of 2ul 10x Tail stop solution. After an RNeasy Minelute cleanup step and elution into 18ul of water, chemical fragmentation using the NEBnext Magnesium RNA Fragmentation kit (NEB) was performed in 20ul for 3.5min at 94C. Afterwards, the reaction was immediately put on ice, and 2ul of RNA Fragmentation Stop Solution was added. Another RNeasy Minelute cleanup step was performed, eluting into 15ul of water. cDNA synthesis: 1ul TTTTVN (16.7uM) and 1ul CCCCCCTT (50uM) custom primers (both Sigma) were added to the 15ul fragmented RNA, primed by incubation at 65C for 5min and put on ice. 1st strand cDNA synthesis was performed using the 1st strand mastermix (Illumina Truseq RNA kit) and SuperscriptII enzyme (Life Technologies) by incubating at 25C for 10min, 42C for 50min at 70C for 15min, and cooled to 4C in a MJ-Mini thermocycler (Biorad). 2nd strand synthesis was performed by addition of 25ul 2nd strand master mix and incubation for 1h at 16C. NGS library preparation: An AMPure XP (Beckman Coulter) cleanup step was performed by adding 90ul AMPure XP beads, vortexing and incubating for 15min at RT. After separation on a magnet, the supernatant was removed and the beads were washed twice with 200ul 80% ethanol. After air drying for 10min at RT, cDNA was eluted in 50ul Resuspension buffer and stored at -20C. End repair was performed by adding 10ul Resuspension buffer and 40ul Endrepair mix and incubating at 30C for 30min at 750rpm in a thermomixer (Eppendorf). After another AMPure XP cleanup step using 160ul beads and eluting into 17.5ul Resuspension buffer, the A-overhang addition step was performed. 12.5ul A-tailing mix were added and incubated at 37C for 30min at 750rpm, followed by 5min at 70C and put on ice. Adapter ligation used 2.5ul of a 1:40 dilution of Adapter oligo mix (Agilent Sureselect v4 kit), 2.5ul Resuspension solution and 2.5ul DNA ligase mix, incubated at 30C for 10min in a water bath and stopped by addition of 5ul Stop ligase mix. Adapter ligated cDNA library was cleaned up by 2 rounds of AMPure XP using first 42ul of AMPure XP beads and eluting in 50ul Resuspension buffer and then using 50ul AMPure XP beads and eluting in 40ul Resuspension buffer. Next, a size selection step was performed to create 4 technical replicates between 300-325bp, 325-350bp, 400-425bp and 425-450bp. For this, the purified adapter ligated cDNA was loaded on a 1.5% Agarose gel and separated for 2h at 120V. Using SybrSafe (Invitrogen) as dye and a Dark Reader transilluminator (Clare Chemical Research), narrow bands were cut using 100bp marker as guidance and gel extracted using the Nucleospin Gel and PCR Cleanup kit (Macherey-Nagel) and eluted in 22ul NE buffer. Two sequential rounds of PCR were performed to introduce barcodes and amplify the cDNA library. First, the Sureselect primer and Sureselect ILM Indexing Pre-Capture PCR reverse primer were used with the Phusion HF 2x mix in 50ul in a MJ Mini thermocycler as follows: 2min 98C, followed by 5 cycles of 30sex 98C, 30sec 65C, 1min at 72C, and a final 72C step for 10min. Next, an AMPure XP cleanup step was performed using 90ul AMPure XP beads and eluting into 23ul water. Afterwards, a 2nd PCR was performed using the Sureselect ILM Indexing Post Capture Forward PCR primer and a different PCR Primer Index primer/sample together with the Phusion HF 2x mix in 50ul in a MJ Mini thermocycler as follows: 2min 98C, followed by 13-15 cycles of 30sex 98C, 30sec 57C, 1min at 72C, and a final 72C step for 10min. After a final AMPure XP cleanup step using 90ul beads, the final library was eluted in 20ul water, quantified with the Qubit HS dsDNA kit and pooled equimolarly.

characteristic: description

text: wild type

characteristic: genotype

characteristic: individual

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: fresh specimen

characteristic: specimen with known storage state

characteristic: strain

characteristic: title


text: EMBL European Bioinformatics Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: baker's yeast

characteristic: common name

text: delta-ccr4/pan2 mutant

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: fresh specimen


text: male

characteristic: ArrayExpress-Sex

text: Homo sapiens

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: human

text: Homo sapiens

text: Pooled PCR products

characteristic: sample description

text: Homo sapiens


text: Pharyngula Prim 5 - Prim 25 : ZFS:0000029 - ZFS:0000031

characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from mitfa, allele w2 clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TGCTGATA) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from mitfa, allele w2 clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TAGACGGA) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from mitfa, allele w2 clutch 1 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TGTGAAGA) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from mitfa, allele w2 clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TCTCTTCA) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from mitfa, allele w2 clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TTGTTCCA) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from mitfa, allele w2 clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TGAAGCCA) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from mitfa, allele w2 clutch 2 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TACCACCA) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from mitfa, allele w2 clutch 3 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (TGCGTGAA) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from mitfa, allele w2 clutch 3 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GGTGAGTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from mitfa, allele w2 clutch 3 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GATCTCTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from mitfa, allele w2 clutch 3 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GTGTCCTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from mitfa, allele w2 clutch 4 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GCAACATT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-CHECKLIST

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from mitfa, allele w2 clutch 4 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GGTCGTGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from mitfa, allele w2 clutch 4 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GAATCTGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from mitfa, allele w2 clutch 5 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GTACATCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from mitfa, allele w2 clutch 5 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GAGGTGCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Pharyngula Prim 5 - Prim 25 : ZFS:0000029 - ZFS:0000031

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from mitfa, allele w2 clutch 5 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GCATGGCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically normal zebrafish embryo from mitfa, allele w2 clutch 6 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GTTAGCCT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from single morphologically abnormal zebrafish embryo from mitfa, allele w2 clutch 6 plus ERCC spike mix 2 (Ambion). A 8 base indexing sequence (GTCGCTAT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Mus musculus

text: SC

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: Mus musculus


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at zygote - 1 cell stage (0 hpf). A 8 base indexing sequence (ATCACGTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at zygote - 1 cell stage (0 hpf). A 8 base indexing sequence (CGATGTTT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at zygote - 1 cell stage (0 hpf). A 8 base indexing sequence (TTAGGCAT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at zygote - 1 cell stage (0 hpf). A 8 base indexing sequence (TGACCACT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at zygote - 1 cell stage (0 hpf). A 8 base indexing sequence (ACAGTGGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at zygote - 1 cell stage (0 hpf). A 8 base indexing sequence (GCCAATGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at zygote - 1 cell stage (0 hpf). A 8 base indexing sequence (CAGATCTG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at zygote - 1 cell stage (0 hpf). A 8 base indexing sequence (ACTTGATG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at zygote - 1 cell stage (0 hpf). A 8 base indexing sequence (GATCAGCG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Whole Embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at zygote - 1 cell stage (0 hpf). A 8 base indexing sequence (TAGCTTGT) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed

characteristic: strain


text: Whole Embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from wild type zebrafish embryo pools collected at zygote - 1 cell stage (0 hpf). A 8 base indexing sequence (GGCTACAG) is bases 11 to 18 of non-index read 2 followed by CG and polyT.

text: Danio rerio

text: mixed