text: Haemonchus contortus

characteristic: ArrayExpress-Species

text: Swiss

text: SC

text: public

text: barber pole worm

text: Haemonchus contortus

text: Haemonchus contortus

text: Swiss


status: PUBLIC

text: Haemonchus contortus

tag: attribute

text: UK Farm 95

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: barber pole worm

characteristic: common name

text: Haemonchus contortus

characteristic: organism

text: Haemonchus contortus

text: UK Farm 95

characteristic: strain


text: Plasmodium falciparum

text: SC

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: IPK-Gatersleben

text: public

text: domesticated barley

text: Sequencing of barley BACs

characteristic: description

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

characteristic: title


text: Liver

characteristic: ArrayExpress-OrganismPart

text: Japanese rice fish

characteristic: ArrayExpress-Species

text: SC

text: public

text: Japanese medaka

text: Oryzias latipes

text: Total RNA from liver cells

characteristic: sample description

text: Oryzias latipes


text: Liver

text: Japanses rice fish

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Japanese medaka

text: Oryzias latipes

text: Total RNA from liver cells

text: Oryzias latipes


text: Japanese rice fish

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: Japanese medaka

text: Oryzias latipes

text: Total RNA from liver cells

text: Oryzias latipes


E-MTAB-3636:Sample 1

text: Harvard Medical School

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-3636:Sample 1

tag: Namespace:Harvard Medical School

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Brain tissues were dissected from E13.5 Swiss Webster mouse brains. CLIP experiments were performed with E14 Swiss Webster mouse brains as described (Ule 2003; Ule 2005; Licatalosi 2008; Preitner 2014). Briefly, embryonic brain tissues were partially dissociated before UV irradiation (UV at 254 nm, 3X 300 mJ/cm2 in a Stratalinker). Cell lysates were sonicated, treated with DNase, and digested with benzonase (Sigma E8263; at a final dilution of 1:2000; 10 min at 37°C) to produce protein-bound RNAs of ~40 nt fragments. Then pre-cleared lysates were mixed with 30 μl Sepharose beads and 30 μg antibody (mouse polyclonal anti-IMP2 antibody, Abnova H00010644-A01; rabbit anti-IMP2 antibody, Proteintech 11601-1-AP), and rotated for 3 hours at 4°C. Immunoprecipitated protein-RNA complexes were stringently washed with SDS- containing buffer and dephosphorylated, and the radiolabeled RNA adapter (5’- UCGUAUGCCGUCUUCUGCUUGU-3’) were ligated at the 3’ end of the RNA fragments. Protein-RNA complexes were then phosphorylated at the 5’ end, separated on a 4-12% denaturing NuPAGE gel (Invitrogen), transferred to a nitrocellulose membrane, and exposed on a film. Narrow bands corresponding to the size of the specific protein-RNA complexes were then excised from the membrane. RNA fragments were extracted, ligated to the 5’ adapter (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’) and amplified by RT-PCR (primers: AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA, and CAAGCAGAAGACGGCATACGA). The purified PCR products were sequenced on Illumina sequencing platform.

text: embryonic day 13.5

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: brain

characteristic: organism part

text: Mus musculus

text: Swiss Webster

text: Sample 1

type: has member


E-MTAB-3636:Sample 2

text: Harvard Medical School

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3636:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: common name

text: embryonic day 13.5

text: Mus musculus

text: Mus musculus

text: brain

text: Mus musculus

text: Swiss Webster

text: Sample 2


E-MTAB-3636:Sample 3

text: Harvard Medical School

text: public

text: E-MTAB-3636:Sample 3

text: ArrayExpress

text: house mouse

characteristic: description

text: embryonic day 13.5

text: Mus musculus

characteristic: organism

text: Mus musculus

text: brain

text: Mus musculus

text: Swiss Webster

characteristic: strain

text: Sample 3

characteristic: title


E-MTAB-3636:Sample 4

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Harvard Medical School

text: public

text: E-MTAB-3636:Sample 4

text: ArrayExpress

text: house mouse

text: embryonic day 13.5

text: Mus musculus

text: Mus musculus

text: brain

text: Mus musculus

text: Swiss Webster

text: Sample 4


E-MTAB-3636:Sample 5

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Harvard Medical School

text: public

text: E-MTAB-3636:Sample 5

text: ArrayExpress

text: house mouse

text: Protocols: Brain tissues were dissected from E13.5 Swiss Webster mouse brains. Polyadenylated RNAs from E13.5 mouse brains were isolated and sequenced.

text: embryonic day 13.5

text: Mus musculus

text: Mus musculus

text: brain

text: Mus musculus

text: Swiss Webster

text: Sample 5


characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:oregon state university , corvallis, oregon, united states

text: ArrayExpress

text: house mouse

text: Protocols: NA NA NA

text: IFNg knock out

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: ileum

text: Mus musculus


text: oregon state university , corvallis, oregon, united states

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: NA NA NA

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: ileum

characteristic: organism part

text: Mus musculus


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

text: Protocols: NA NA NA

text: IFNg knock out

text: Mus musculus

text: Mus musculus

text: ileum

text: Mus musculus


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: Protocols: NA NA NA

text: IFNg knock out

text: Akkermansia muciniphila

characteristic: infect

text: Mus musculus

text: Mus musculus

text: ileum

text: Mus musculus


text: UCL

text: public

text: ArrayExpress

text: common frog

characteristic: common name

text: Protocols: R. temporaria eggs were obtained from a private garden pond in Chessington in the UK with the permission of the landowner. This site has a known history of Ranavirus infection, but an unknown history of Bd infection. The eggs were hatched and reared through metamorphosis under controlled conditions, showing good survival and no signs of infection. Metamorphs (n = 45) were moved into an experimental room (18-21ºC, 33-46% humidity, full spectrum UV light) for acclimatisation one week prior to exposure, and were placed in individual boxes and fed on crickets ad libitum. Livers were used because they are large, easily targeted organs which are important for immunity and are a target organ in ranavirus disease. Livers were immediately dissected, preserved individually in RNAlater solution (Sigma Aldrich), and stored at -80ºC. Ranavirus (RUK13 isolate) was cultured at 24ºC in Fathead Minnow cells (FHM, Epithelial-like cells from the posterior anal tissue, obtained from the European Collection of Cell Cultures catalogue number 88102401) in maintenance media (EMEM + 10% FBS + 1% L-Glutamine) and quantified on 96 well flat-bottomed cell culture plates using the TCID50 method. Bd inoculum (Isolate IA 042, BdGPL) was prepared by culture in mTGhL medium at 18ºC for four days before counting zoospores using a haemocytometer. This work was carried out under Home Office license (Project Licence numbers PPL 80/2214 and PPL 80/2466) and was approved by the Institute of Zoology Ethics Committee and the University of Exeter Ethical Review Board. In total 45 frogs were used - 15 animals for each of three exposure treatments (Ranavirus, Bd, Control). Animals were checked, cleaned and given fresh water frequently whilst being mindful of causing them distress through unnecessary handling. Exposure was performed in individual tubes with 29ml aged tap water with 1ml of inoculum (Ranavirus at 1k TCID50/ml or Bd at 100k active zoospores/ml), or 30ml tap water for the control treatment, for four hours. Following exposure, the frogs were returned to their individual boxes and examined daily for signs of Ranavirus infection (oedema of the eye, skin ulceration, bleeding), which would have served as an endpoint for the experiment but none were observed. Frogs were euthanized according to Schedule 1 to the Animals (Scientific Procedures) Act 1986 four days post-exposure by immersion in fresh 5g/L Tricaine methane sulphonate (MS222, Pharmaq Ltd.) solution neutralized with sodium bicarbonate in accordance with Universities Federation for Animal Welfare guidance to ameliorate suffering. Total RNA was extracted from 5-20µg of liver tissue using the Qiagen RNeasy Mini Kit (Qiagen, Valencia USA) using the standard protocol. Each treatment consisted of 15 frogs; three pools were sequenced per treatment, with five individuals per pool. We therefore prepared nine samples for sequencing; 3 replicates per treatment, each consisting of pooled RNA extracted from the livers of 5 individuals. RNA concentration was estimated using a NanoDrop (NanoDrop, Wilmington USA), and concentrations of individual sample extractions were equalized within pools, resulting in a total pool volume of 80µl (concentrations varied between pools). The sample concentrations were not normalized. 1µl ERCC spike in control mix (Invitrogen) was added to each sample before library preparation. Poly-A-RNA was isolated and barcoded RNAseq libraries were prepared using ScriptSeq v2 (Epicentre) with 15 cycles PCR amplification. Equimolar amounts of two libraries were pooled denatured and diluted to 6 pM

characteristic: description

text: metamorph

characteristic: developmental stage

text: Rana temporaria

characteristic: organism

text: Rana temporaria

text: liver

text: Rana temporaria

text: Batrachochytrium dendrobatidis exposure

characteristic: stimulus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UCL

text: public

text: ArrayExpress

text: common frog

text: metamorph

text: Rana temporaria

text: Rana temporaria

text: liver

text: Rana temporaria

text: Mock exposure

characteristic: title


characteristic: External Id

text: UCL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: common frog

text: metamorph

text: Rana temporaria

text: Rana temporaria

text: liver

text: Rana temporaria

text: Ranavirus exposure


text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC last update

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:'Eric So lab Leukaemia and Stem Cell Biology Group Department of Haematological Medicine King''s College London'

text: ArrayExpress

characteristic: broker name

text: granulocyte monocyte progenitor cell

characteristic: cell type

text: house mouse

text: Protocols: Ctnnb1fl/fl mice were crossed with Rosa26-CreER Rosa26-YFP mice to generate Ctnnb1fl/fl RosaCre-ER RosaYFP mice. These mice were crossed with Hoxa9-/- knockout mice to generate Hoxa9-/- Ctnnb1fl/fl RosaCre-ER RosaYFP mice. Compound homozygous animals were used for experiments. For leukemia development experiments, C57BL/6 or SJL mice were given 11Gy total body Îł-irradiation and injected with up to 500,000 test cells mixed with 200,000 C57BL/6 or SJL bone marrow nuclear cells. LSK (lin-, Sca-1+, c-Kit+) and GMP (lin-, Sca-1-, c-Kit+, CD34+, CD16/32lo) were isolated from lineage negative cells after lineage (Gr-1, Mac-1, B220, Ter119, CD3e, CD4, CD8) depletion using a BD FACS ARIA cell sorter. 300ng to 1ug of mIRVANA (Ambion) isolated total RNA was used for RNA-Seq library preparation using TruSeq Stranded Total RNA kit (Illumina).

text: acute myeloid leukemia

characteristic: disease

text: Ctnnb1 knock-out

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: MLL-ENL

characteristic: transfection


characteristic: ENA-CHECKLIST

text: 'Eric So lab Leukaemia and Stem Cell Biology Group Department of Haematological Medicine King''s College London'

text: public

characteristic: Submitter Id

text: ArrayExpress

text: granulocyte monocyte progenitor cell

text: house mouse

characteristic: common name

characteristic: description

text: acute myeloid leukemia

text: Ctnnb1 knock-out

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: MLL-ENL


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: granulocyte monocyte progenitor cell

text: house mouse

text: acute myeloid leukemia

text: floxed

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title

text: MLL-ENL


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: granulocyte monocyte progenitor cell

text: house mouse

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus


text: public

text: ArrayExpress

characteristic: broker name

text: hematopoietic stem cell

characteristic: cell type

text: house mouse

text: acute myeloid leukemia

characteristic: disease

text: Ctnnb1 knock-out

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: MLL-ENL


characteristic: ENA-CHECKLIST

text: public

characteristic: Submitter Id

text: ArrayExpress

text: hematopoietic stem cell

text: house mouse

text: acute myeloid leukemia

text: Ctnnb1 and Hoxa9 knock-out

characteristic: individual

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: MLL-ENL

characteristic: transfection


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: hematopoietic stem cell

text: house mouse

characteristic: common name

characteristic: description

text: acute myeloid leukemia

text: Hoxa9 knock-out

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: MLL-ENL


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: hematopoietic stem cell

text: house mouse

text: acute myeloid leukemia

text: floxed

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: title

text: MLL-ENL


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: hematopoietic stem cell

text: house mouse

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus


E-MTAB-3662:DW133 WNG011.fastq.gz

text: EMBL-EBI

text: public

text: E-MTAB-3662:DW133 WNG011.fastq.gz

text: 16 week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: as described in Wang L, Si Y, Dedow LK, Shao Y, Liu P, et al. (2011) A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand- Specific Multiplex RNA-Seq. PLoS ONE 6(10): e26426. doi:10.1371/journal.pone.0026426 As described in Wang L, Si Y, Dedow LK, Shao Y, Liu P, et al. (2011) A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand- Specific Multiplex RNA-Seq. PLoS ONE 6(10): e26426. doi:10.1371/journal.pone.0026426

text: Arl10 Knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: cardiac ventricle

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: C57BL/6 BL1672

characteristic: strain

text: DW133 WNG011.fastq.gz


E-MTAB-3662:DW120 WNG011.fastq.gz

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL-EBI

text: public

text: E-MTAB-3662:DW120 WNG011.fastq.gz

characteristic: Submitter Id

text: 16 week

text: ArrayExpress

text: house mouse

characteristic: common name

text: Klf14 Knockout

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

text: C57BL/6 BL1129

text: DW120 WNG011.fastq.gz


E-MTAB-3662:DW112 WNG007.fastq.gz

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL-EBI

text: public

text: E-MTAB-3662:DW112 WNG007.fastq.gz

text: 16 week

text: ArrayExpress

text: house mouse

characteristic: description

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cardiac ventricle

text: Mus musculus

text: male

text: C57BL/6 controls

text: DW112 WNG007.fastq.gz


E-MTAB-3662:DW133 WNG013.fastq.gz

text: EMBL-EBI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3662:DW133 WNG013.fastq.gz

text: 16 week

text: ArrayExpress

text: house mouse

text: Arl10 Knockout

text: Mus musculus

text: Mus musculus

text: cardiac ventricle

text: Mus musculus

text: male

text: C57BL/6 BL1672

text: DW133 WNG013.fastq.gz

characteristic: title


E-MTAB-3662:DW113 WNG002.fastq.gz

text: EMBL-EBI

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3662:DW113 WNG002.fastq.gz

text: 16 week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

text: C57BL/6 controls

text: DW113 WNG002.fastq.gz


E-MTAB-3662:DW113 WNG007.fastq.gz

text: EMBL-EBI

text: public

text: E-MTAB-3662:DW113 WNG007.fastq.gz

text: 16 week

text: ArrayExpress

text: house mouse

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: C57BL/6 controls

characteristic: strain

text: DW113 WNG007.fastq.gz


E-MTAB-3662:DW120 WNG014.fastq.gz

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL-EBI

text: public

text: E-MTAB-3662:DW120 WNG014.fastq.gz

characteristic: Submitter Id

text: 16 week

text: ArrayExpress

text: house mouse

characteristic: common name

text: Klf14 Knockout

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

text: C57BL/6 BL1129

text: DW120 WNG014.fastq.gz


E-MTAB-3662:DW133 WNG010.fastq.gz

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL-EBI

text: public

text: E-MTAB-3662:DW133 WNG010.fastq.gz

text: 16 week

text: ArrayExpress

text: house mouse

characteristic: description

text: Arl10 Knockout

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cardiac ventricle

text: Mus musculus

text: male

text: C57BL/6 BL1672

text: DW133 WNG010.fastq.gz


E-MTAB-3662:DW112 WNG008.fastq.gz

text: EMBL-EBI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3662:DW112 WNG008.fastq.gz

text: 16 week

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: cardiac ventricle

text: Mus musculus

text: male

text: C57BL/6 controls

text: DW112 WNG008.fastq.gz

characteristic: title


E-MTAB-3662:DW120 WNG013.fastq.gz

text: EMBL-EBI

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3662:DW120 WNG013.fastq.gz

text: 16 week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Klf14 Knockout

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

text: C57BL/6 BL1129

text: DW120 WNG013.fastq.gz


E-MTAB-3662:DW113 WNG010.fastq.gz

text: EMBL-EBI

text: public

text: E-MTAB-3662:DW113 WNG010.fastq.gz

text: 16 week

text: ArrayExpress

text: house mouse

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: C57BL/6 controls

characteristic: strain

text: DW113 WNG010.fastq.gz


E-MTAB-3662:DW112 WNG006.fastq.gz

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL-EBI

text: public

text: E-MTAB-3662:DW112 WNG006.fastq.gz

characteristic: Submitter Id

text: 16 week

text: ArrayExpress

text: house mouse

characteristic: common name

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: cardiac ventricle

text: Mus musculus

text: male

text: C57BL/6 controls

text: DW112 WNG006.fastq.gz


E-MTAB-3662:DW113 WNG008.fastq.gz

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL-EBI

text: public

text: E-MTAB-3662:DW113 WNG008.fastq.gz

text: 16 week

text: ArrayExpress

text: house mouse

characteristic: description

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: male

text: C57BL/6 controls

text: DW113 WNG008.fastq.gz


E-MTAB-3662:DW113 WNG001.fastq.gz

text: EMBL-EBI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3662:DW113 WNG001.fastq.gz

text: 16 week

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

text: C57BL/6 controls

text: DW113 WNG001.fastq.gz

characteristic: title


E-MTAB-3662:DW112 WNG001.fastq.gz

text: EMBL-EBI

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3662:DW112 WNG001.fastq.gz

text: 16 week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: cardiac ventricle

text: Mus musculus

text: male

text: C57BL/6 controls

text: DW112 WNG001.fastq.gz


text: EMBL Heidelberg

text: public

tag: Namespace:EMBL Heidelberg

characteristic: batch

text: ArrayExpress

text: medullary thymic epithelial cell

characteristic: cell type

text: house mouse

text: Protocols: Human mTECs were processed as in Pinto et al, 2013. Mouse mTECs were isolated and purified as described previously (Rattay et al, 2015). The pre-enriched stromal cell fraction, sorted for total mTECs (n = 259 cells) was stained using the following antibodies: anti-CD45-PerCP (clone 30-F11, BD Pharmingen), anti-EpCAM-Alexa647 (G8.8, described by Farr et al ), anti-CDR1-Pacific Blue or anti-Ly51-FITC (CDR1 hybridoma, described by Rouse et al ; clone 6C3, BD Biosciences). For the antigen-specific mTECs Tspan8 (n = 48) and Ceacam1 (n = 30) additional antibodies were added to the antibody mix namely: anti-I-A(b)-FITC (clone AF6-120.1, BD Pharmingen), anti-Tspan8-PE (clone 657909, RandD Systems) and anti-CD66a-PE (i.e., anti-Ceacam1, clone CC1, eBioscience). Dead cells were excluded using propidium iodide (PI) in a final concentration of 0.2 ug/ml. Cells were sorted on BD FACSAria(TM) III cell sorter (BD Biosciences) using the single-cell sorting mode as previously described (Derbinski et al, 2008) We used a modified version of Smrt-seq2. We used 19 cycles of initial PCR amplification and used a ratio of 0.6:1 (instead of a 1:1 ratio) of Ampure XP beads (Beckman Coulter) for the first PCR purification to minimize primer dimer carryover. After the first PCR amplification, cDNA libraries were screened via qPCR (we used a 1:10 dilution of purified cDNA libraries for qPCR reactions) for expression of a mouse housekeeping gene (Ubc), and library size distribution was checked on the Bioanalyzer instrument (Agilent) as reported previously . Only cDNA libraries that passed both quality controls were processed further. We used 100 pg of cDNA for the tagmentation reaction and applied 12 cycles for the final enrichment PCR of adapter-ligated fragments. The last purification step was performed using a 0.8:1 ratio of Ampure SPRIselect beads (Beckman Coulter).

text: Mus musculus

text: Mus musculus

text: PI(neg)CD45(neg)Ly51(neg)EpCAM(pos)MHCII(high)Klk5(qPCR-pos)

characteristic: phenotype

text: Mus musculus

text: OK

characteristic: single cell well quality


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL Heidelberg

text: public

characteristic: Submitter Id

text: AtacHiCov

text: ArrayExpress

text: medullary thymic epithelial cell

text: human

characteristic: common name

text: Protocols: Human mTECs were processed as in Pinto et al, 2013. Mouse mTECs were isolated and purified as described previously (Rattay et al, 2015). The pre-enriched stromal cell fraction, sorted for total mTECs (n = 259 cells) was stained using the following antibodies: anti-CD45-PerCP (clone 30-F11, BD Pharmingen), anti-EpCAM-Alexa647 (G8.8, described by Farr et al ), anti-CDR1-Pacific Blue or anti-Ly51-FITC (CDR1 hybridoma, described by Rouse et al ; clone 6C3, BD Biosciences). For the antigen-specific mTECs Tspan8 (n = 48) and Ceacam1 (n = 30) additional antibodies were added to the antibody mix namely: anti-I-A(b)-FITC (clone AF6-120.1, BD Pharmingen), anti-Tspan8-PE (clone 657909, RandD Systems) and anti-CD66a-PE (i.e., anti-Ceacam1, clone CC1, eBioscience). Dead cells were excluded using propidium iodide (PI) in a final concentration of 0.2 ug/ml. Cells were sorted on BD FACSAria(TM) III cell sorter (BD Biosciences) using the single-cell sorting mode as previously described (Derbinski et al, 2008) Human mTEC subsets (surface TRA positive and surface TRA depleted cells) were isolated and FACS sorted as described elsewhere(Pinto et al, 2013). ATAC-seq experiments were performed as reported previously (Buenrostro et al) with the following modifications: 15,000 â 50,000 pooled cells (depending on mTEC subset frequencies) were sorted in PBS (5 percent FCS) and used for ATAC-seq experiments. We used 50 percent of each purified tagmentation reaction for the enrichment PCR (without 5 cycle pre-amplification). Enrichment PCRs were monitored individually using a StepOnePlus Real-Time PCR System (Life Technologies) and the amplification reaction was stopped as soon as amplification approached saturation. After the enrichment PCR, we performed a gel extraction (QIAquick Gel Extraction Kit, QIAGEN) to remove primer dimer.

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Mouse

characteristic: ArrayExpress-Phenotype

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus


text: Normal;

text: Mus musculus

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: Mus musculus


text: public

characteristic: SRA accession

text: human

text: ES2 human ovarian cancer cell line

characteristic: description

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: public

text: human

text: HCH1 human ovarian cancer cell line

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: KOC7C human ovarian cancer cell line

text: Homo sapiens

text: Homo sapiens


OVAS

text: public

text: OVAS

text: human

text: OVAS human ovarian cancer cell line

text: Homo sapiens

text: Homo sapiens

text: OVAS


OVISE

text: public

text: OVISE

text: human

text: OVISE human ovarian cancer cell line

text: Homo sapiens

text: Homo sapiens

text: OVISE


OVMANA

text: public

text: OVMANA

text: human

text: OVMANA human ovarian cancer cell line

text: Homo sapiens

text: Homo sapiens

text: OVMANA


OVSAYO

text: public

text: OVSAYO

text: human

text: OVSAYO human ovarian cancer cell line

text: Homo sapiens

text: Homo sapiens

text: OVSAYO


OVTOKO

text: public

text: OVTOKO

text: human

text: OVTOKO human ovarian cancer cell line

text: Homo sapiens

text: Homo sapiens

text: OVTOKO


RMGI

text: public

text: RMGI

text: human

text: RMGI human ovarian cancer cell line

text: Homo sapiens

text: Homo sapiens

text: RMGI


text: public

text: human

text: SMOV2 human ovarian cancer cell line

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: TOV21G human ovarian cancer cell line

text: Homo sapiens

text: Homo sapiens


text: Pharyngula:Prim-5 - Pharyngula:Prim-15 - ZFS:0000029 - ZFS:0000030

characteristic: ArrayExpress-DevelopmentalStage

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 a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (ATCACGTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (CGATGTTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TTAGGCAT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TGACCACT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (ACAGTGGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

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 a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (GCCAATGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (CAGATCTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (ACTTGATG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (GATCAGCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TAGCTTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (GGCTACAG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

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 a single genotyped zebrafish embryo homozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (CTTGTACT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

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 a single genotyped zebrafish embryo heterozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TGGTTGTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo heterozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TCTCGGTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

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 a single genotyped zebrafish embryo heterozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TAAGCGTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo heterozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TCCGTCTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Pharyngula:Prim-5 - Pharyngula:Prim-15 - ZFS:0000029 - ZFS:0000030

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo heterozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TGTACCTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo heterozygous for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TTCTGTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo wild type for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TCTGCTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single genotyped zebrafish embryo wild type for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TTGGAGGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

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 a single genotyped zebrafish embryo wild type for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TCGAGCGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

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 a single genotyped zebrafish embryo wild type for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TGATACGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single genotyped zebrafish embryo wild type for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TGCATAGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

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 a single genotyped zebrafish embryo wild type for dicer, allele sa9205 from ZMP phenotype 182 clutch 1, plus ERCC spike mix 2. A 8 base indexing sequence (TTGACTCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph182

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_156_1_phenotypic_1-sc-2318187

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 156 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (ATCACGTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph156

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: ZMP_phenotype_156_1_phenotypic_2-sc-2318188

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 156 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (CGATGTTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph156

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_156_1_phenotypic_3-sc-2318189

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 156 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (TTAGGCAT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph156

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: ZMP_phenotype_156_1_phenotypic_4-sc-2318190

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 156 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (TGACCACT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph156

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

text: public

text: ZMP_phenotype_156_1_phenotypic_5-sc-2318191

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 156 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (ACAGTGGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph156

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ZMP_phenotype_156_1_phenotypic_6-sc-2318192

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 156 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (GCCAATGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph156

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ZMP_phenotype_156_1_phenotypic_7-sc-2318193

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 156 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (CAGATCTG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph156

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: ZMP_phenotype_156_1_phenotypic_8-sc-2318194

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 156 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (ACTTGATG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph156

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: ZMP_phenotype_156_1_phenotypic_9-sc-2318195

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 156 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (GATCAGCG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph156

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_156_1_phenotypic_10-sc-2318196

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 156 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (TAGCTTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph156

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: ZMP_phenotype_156_1_phenotypic_11-sc-2318197

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 156 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (GGCTACAG) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph156

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_156_1_phenotypic_12-sc-2318198

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically abnormal embryo from ZMP phenotype 156 clutch 1 obtained by crossing two fish homozygous for tert, allele sa6541. The homozygous adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter homozygous fish from the clutch.A 8 base indexing sequence (CTTGTACT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph156

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: ZMP_phenotype_224_1_non_phenotypic_1-sc-2318199

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 224 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TGGTTGTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph224

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

text: public

text: ZMP_phenotype_224_1_non_phenotypic_2-sc-2318200

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 224 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TCTCGGTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph224

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ZMP_phenotype_224_1_non_phenotypic_3-sc-2318201

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 224 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TAAGCGTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph224

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ZMP_phenotype_224_1_non_phenotypic_4-sc-2318202

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 224 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TCCGTCTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph224

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

text: ZMP_phenotype_224_1_non_phenotypic_5-sc-2318203

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 224 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TGTACCTT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph224

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: ZMP_phenotype_224_1_non_phenotypic_6-sc-2318204

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 224 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TTCTGTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph224

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_224_1_non_phenotypic_7-sc-2318205

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 224 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TCTGCTGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph224

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: ZMP_phenotype_224_1_non_phenotypic_8-sc-2318206

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 224 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TTGGAGGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph224

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: ZMP_phenotype_224_1_non_phenotypic_9-sc-2318207

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 224 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TCGAGCGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph224

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: ZMP_phenotype_224_1_non_phenotypic_10-sc-2318208

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 224 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TGATACGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph224

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: External Id

text: SC

text: public

text: ZMP_phenotype_224_1_non_phenotypic_11-sc-2318209

text: zebrafish

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 224 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TGCATAGT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph224

text: Danio rerio

text: mixed


text: Pharyngula:Prim-5 - ZFS:0000029

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ZMP_phenotype_224_1_non_phenotypic_12-sc-2318210

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single phenotypically normal embryo from ZMP phenotype 224 clutch 1 obtained by crossing two fish wild type for tert, allele sa6541. The wild type adults were obtained by crossing parents heterozygous for tert, sa6541 and growing the quarter wild type fish from the clutch.A 8 base indexing sequence (TTGACTCT) is bases 13 to 20 of read 1 followed by CG and polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph224

text: Danio rerio

text: mixed


text: Haemonchus contortus

text: ISE

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: barber pole worm

text: Haemonchus contortus

text: Haemonchus contortus

text: ISE


text: mus musculus

text: SC

text: public

characteristic: SRA accession

text: house mouse

text: Mus musculus

text: Screen 12 Unstimulated Wild Type Knock-out Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 6 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Wild Type Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Unstimulated Wild Type Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Unstimulated Ikbkb Knock-out Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Ikbkb Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Ikbkb Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Ikbkb Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Ikbkb Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Ikbkb Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Ikbkb Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 6 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Ikbkb Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Unstimulated Ikbkb Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Unstimulated Irf1 Knock-out Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 6 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Irf1 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Unstimulated Irf1 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Unstimulated Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Poly I:C (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with ODN 1826 (CpG)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with M TRI-dap (NOD agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with LPS (Toll-like receptor agonist)

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 6 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Influenza 24 hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Unstimulated Mapk14 Knock-out Embryonic Stem Cell Derived Macrophages 24hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Unstimulated Lmnb2 Knock-out Embryonic Stem Cell Derived Macrophages 4hr

text: Mus musculus


text: mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Screen 12 Lmnb2 Knock-out Embryonic Stem Cell Derived Macrophages stimulated with Salmonella

text: Mus musculus


text: Haemonchus contortus

text: ISE

text: SC

text: public

text: barber pole worm

text: Haemonchus contortus

text: Haemonchus contortus

text: ISE


text: IPK-Gatersleben

text: public

text: domesticated barley

text: Sequencing of barley BACs, that constitute the MTP of chromosome 3H

characteristic: description

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

characteristic: title


text: Homo Sapien

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: Mouse Lung

characteristic: ArrayExpress-OrganismPart

text: Mouse Lung

characteristic: ArrayExpress-Phenotype

text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Total RNA

characteristic: sample description

text: Mus musculus


status: KILLED

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY DUISBURG-ESSEN

text: killed

tag: Namespace:UNIVERSITY DUISBURG-ESSEN

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 1


text: UNIVERSITY DUISBURG-ESSEN

text: killed

characteristic: Submitter Id

text: human

characteristic: common name

text: primary tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 1


characteristic: ENA-LAST-UPDATE

text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 1


characteristic: External Id

text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 3


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: primary tumor

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Neuroblastoma Tumor 3


text: UNIVERSITY DUISBURG-ESSEN

characteristic: INSDC center name

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 3


text: UNIVERSITY DUISBURG-ESSEN

characteristic: INSDC first public

text: killed

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 4


text: UNIVERSITY DUISBURG-ESSEN

characteristic: INSDC last update

text: killed

text: human

text: primary tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 4


text: UNIVERSITY DUISBURG-ESSEN

text: killed

characteristic: INSDC status

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 4


text: UNIVERSITY DUISBURG-ESSEN

text: killed

characteristic: SRA accession

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 5


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: primary tumor

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 5


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 5

characteristic: title


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 6


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: primary tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 6


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 6


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 7


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: primary tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 7


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 7


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 8


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: primary tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 8


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 8


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 9


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: primary tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 9


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 9


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 10


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: primary tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 10


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 10


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 11


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: primary tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 11


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 11


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 12


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: primary tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 12


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse1 12


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse2 12


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse3 12


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse4 12


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse5 12


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 13


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: primary tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 13


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 13


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 14


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: primary tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 14


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 14


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 15


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: primary tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 15


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 15


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: control

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Control 16


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: primary tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Tumor 16


text: UNIVERSITY DUISBURG-ESSEN

text: killed

text: human

text: relapse tumor

text: Homo sapiens

text: Homo sapiens

text: Neuroblastoma Relapse 16


text: mouse ESC

characteristic: ArrayExpress-CellType

text: cell line

characteristic: ArrayExpress-OrganismPart

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


E-MTAB-3653:Sample 1

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3653:Sample 1

tag: Namespace:Max-Planck-Institute for Biophysical Chemistry, Department of Molecular Biology

text: ArrayExpress

characteristic: broker name

text: fission yeast

text: Protocols: A fresh plate (YES) was inoculated from glycerol stock. An over-night culture was inoculated (YES medium) from a single colony and grown at 30 ???C. In the morning a 120 mL culture (YEA medium) was started at OD600 0.1 and grown to OD600 of 0.8 at 32 ???C in a water bath at 150 rpm. 4-thiouracil was added to 110 mL of culture at 5 mM final concentration. 20 mL samples were taken out after 2, 4, 6, 8, and 10 minutes. Each sample was centrifuged immediately at 32 ???C, at 3,500 rpm for 1 min. The supernatant was discarded and the pellet was frozen in liquid nitrogen. All experiments were performed in two independent biological replicates. Total RNA was extracted and samples were DNase digested with Turbo DNase (Ambion). Labeled RNA was purified as published (Sun et al., 2012). rRNA was depleted using the Ribo-ZeroTM Gold Kit (Yeast, Epicentre) according to the manufacturer???s recommendation with 1.5 ??g labeled RNA and with 2.5 ??g total RNA as input. Sequencing libraries for the time series samples were prepared according to the manufacturer???s recommendations using the ScriptSeq??? v2 RNA-Seq Library Preparation Kit (Epicentre).

text: 4tU RNA

characteristic: fraction

characteristic: labelling

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

unit: minute

characteristic: time

text: Sample 1


E-MTAB-3653:Sample 10

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Max-Planck-Institute for Biophysical Chemistry, Department of Molecular Biology

text: public

text: E-MTAB-3653:Sample 10

characteristic: Submitter Id

text: ArrayExpress

text: fission yeast

characteristic: common name

text: 4tU RNA

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Sample 10


E-MTAB-3653:Sample 11

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-3653:Sample 11

text: ArrayExpress

text: fission yeast

text: Total RNA

text: Schizosaccharomyces pombe

characteristic: organism

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Sample 11


E-MTAB-3653:Sample 12

text: public

characteristic: SRA accession

text: E-MTAB-3653:Sample 12

text: ArrayExpress

text: fission yeast

characteristic: description

text: Total RNA

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Sample 12

characteristic: title


E-MTAB-3653:Sample 13

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3653:Sample 13

text: ArrayExpress

characteristic: broker name

text: fission yeast

text: Total RNA

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Sample 13


E-MTAB-3653:Sample 14

text: public

text: E-MTAB-3653:Sample 14

text: ArrayExpress

text: fission yeast

text: Total RNA

characteristic: fraction

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Sample 14


E-MTAB-3653:Sample 2

text: public

text: E-MTAB-3653:Sample 2

text: ArrayExpress

text: fission yeast

text: 4tU RNA

characteristic: labelling

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

characteristic: time

text: Sample 2


E-MTAB-3653:Sample 3

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-3653:Sample 3

text: ArrayExpress

text: fission yeast

text: 4tU RNA

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Sample 3


E-MTAB-3653:Sample 4

characteristic: External Id

text: public

text: E-MTAB-3653:Sample 4

characteristic: Submitter Id

text: ArrayExpress

text: fission yeast

text: 4tU RNA

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Sample 4


E-MTAB-3653:Sample 5

characteristic: INSDC center name

text: public

text: E-MTAB-3653:Sample 5

text: ArrayExpress

text: fission yeast

characteristic: common name

text: 4tU RNA

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Sample 5


E-MTAB-3653:Sample 6

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-3653:Sample 6

text: ArrayExpress

text: fission yeast

text: 4tU RNA

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Sample 6


E-MTAB-3653:Sample 7

text: public

characteristic: INSDC status

text: E-MTAB-3653:Sample 7

text: ArrayExpress

text: fission yeast

text: 4tU RNA

text: Schizosaccharomyces pombe

characteristic: organism

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Sample 7


E-MTAB-3653:Sample 8

text: public

characteristic: SRA accession

text: E-MTAB-3653:Sample 8

text: ArrayExpress

text: fission yeast

characteristic: description

text: 4tU RNA

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Sample 8


E-MTAB-3653:Sample 9

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-3653:Sample 9

text: ArrayExpress

text: fission yeast

text: 4tU RNA

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: Sample 9

characteristic: title


text: public

tag: Namespace:University of Southern Denmark Department of Biochemistry and Molecular Biology

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Mouse tissues were collected on PND1 and PND5. Mice were sacrificed with CO2 asphyxiation and organs/tissues were rinsed in saline, snap-frozen in liquid N2 and stored in -80°C until processing. For extraction of RNA samples, tissues were pulverized in liquid N2 with a mortar and pestle and total RNA was purified with RNeasy Mini Kit and treated with RNase-free Dnase I. RNA purity, integrity and concentration were determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc, USA). Only RNA with a RIN value of 8.0 or higher and a ratio (28s/18s) of above 1.8 was taken forward for sample preparation. Samples were processed for library constructions following the manufactory instructions (Illumina Tru Seq Stranded Total RNA sample preparation v2 Guide, Part #15031048 Rev.E October 2013 - “Low sample protocol”)*. In brief, 0.5 µg of total RNA from each tissue were depleted for cytoplasmic rRNA using the Ribo-Zero ribosomal reduction chemistry, chemically fragmented for 8 min at 94oC, and processed for 1st strand synthesis cDNA and then 2nd strand synthesis using dUTP instead of dTTP. After some purification steps, the cDNA was then end-repaired, purified, adenylated at the 3’-ends, and purified before adding the indexed adaptor sequences using the TruSeq Stranded LT Kit Index set A. Each library preparation was then enriched by 10 cycles of PCR, purified and finally validated in regards to size and concentration. For sizing, libraries were analyzed on the Agilent 2100 Bioanalyzer using a DNA 1000 kit from Agilent Technologies. The Libraries were quantified by qPCR using the KaPa Library quantification Kits (KaPa Biosystems, Cat KK4824). Samples were pooled in sets of 12 libraries, and a final concentration of 16 pM denatured library was used for paired-end deep sequencing using an Illumina HiSeq1500.

text: heterozygous

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: brain

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Southern Denmark Department of Biochemistry and Molecular Biology

text: public

text: ArrayExpress

text: house mouse

text: heterozygous

text: Mus musculus

text: Mus musculus

text: brain

text: Mus musculus

text: female


characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: common name

text: heterozygous

text: Mus musculus

text: Mus musculus

text: brain

text: Mus musculus

text: male


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

text: spinal muscular atrophy

text: Mus musculus

text: Mus musculus

text: brain

text: Mus musculus

text: female


text: public

characteristic: SRA accession

text: ArrayExpress

text: house mouse

characteristic: description

text: spinal muscular atrophy

text: Mus musculus

characteristic: organism

text: Mus musculus

text: brain

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

text: public

characteristic: age

text: ArrayExpress

text: house mouse

text: heterozygous

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

characteristic: title


text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

text: heterozygous

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: female


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: house mouse

text: spinal muscular atrophy

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: female

characteristic: sex


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: spinal muscular atrophy

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

text: heterozygous

text: Mus musculus

text: Mus musculus

text: muscle

text: Mus musculus

text: male


text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: house mouse

characteristic: description

text: heterozygous

text: Mus musculus

text: Mus musculus

text: muscle

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

text: public

characteristic: age

text: ArrayExpress

text: house mouse

text: spinal muscular atrophy

text: Mus musculus

characteristic: organism

text: Mus musculus

text: muscle

text: Mus musculus

text: female


text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

text: spinal muscular atrophy

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: muscle

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: house mouse

text: Protocols: Mouse tissues were collected on PND1 and PND5. Mice were sacrificed with CO2 asphyxiation and organs/tissues were rinsed in saline, snap-frozen in liquid N2 and stored in -80°C until processing. For extraction of RNA samples, tissues were pulverized in liquid N2 with a mortar and pestle and total RNA was purified with RNeasy Mini Kit and treated with RNase-free Dnase I. RNA purity, integrity and concentration were determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc, USA). Only RNA with a RIN value of 1.8 or higher was taken forward for sample preparation and library construction following the manufactory instructions (Illumina Tru Seq RNA sample preparation v2 Guide, Part #15026495 Rev.B February 2012 - “Low sample protocol”). In brief, 1 µg of total RNA from each mouse was taken forward for library preparation. mRNA was purified, chemically fragmented for 8 min at 94oC, and processed for 1st strand synthesis cDNA and then 2nd strand synthesis. After some purification steps, the cDNA was then end-repaired, purified, adenylated at the 3’-ends, and purified before adding the indexed adaptor sequences. TruSeq RNA sample prep kit v2, set A, cat-RS-122-2001 was used for indexing. Each library preparation was then enriched by 10 cycles of PCR, purified and finally validated in regards to size and concentration. For sizing, libraries were analyzed on the Agilent 2100 Bioanalyzer using a DNA 1000 kit from Agilent Technologies.

text: heterozygous

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: male


characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

text: heterozygous

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

characteristic: sex


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: spinal muscular atrophy

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female


text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: house mouse

characteristic: common name

text: spinal muscular atrophy

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: male