E-MTAB-4014:Sample 28

text: Queen's University Belfast

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-4014:Sample 28

text: ArrayExpress

text: velvet grass

text: Protocols: Plant and soil collection: H. lanatus plants and topsoil were collected from three locations: 6 plants (6 lime genotypes) were selected from a disused limestone quarry soil (pH 7.5) in County Antrim, NI, hereafter referred to as lime, 6 plants (6 acid genotypes) from an acidic peat bog (pH 3.5) in County Tyrone, NI, hereafter referred to as acid, and 6 plants (6 intermediate genotypes) from an acid mineral rough grassland (pH 5.5) (County Down, NI), hereafter refereed to as intermediate. In each case plants were carefully selected within each habitat, with all plants at least 5m apart, so that each of the 6 plants represents a clone for a unique genotype of that particular habitat. Tillers from each plant were trans-planted into John Innes no. 2 compost to nutritionally neutralize all plants. Tillers from compost grown lime and acid ecotypes (5 genotypes each) were subsequently used for set up of a full factorial soil transplant experiment. Tillers from one genotype of each the acid, lime and intermediate population were subsequently grown in hydroponics for additional root acid stress relevant transcriptome sequencing data. Full factorial reciprocal soil transplant experiment: Tillers from 5 genotypes of each the acid and lime ecotype were transplanted from compost onto limestone quarry soil (total 10 pots) and grown in the growth chamber for 7 weeks. Replication was at the level of ecotype by using 5 tillers from 5 different clonal plants from each ecotype (5 genotypes per ecotype) rather than using multiple tillers from one plant, to ensure that natural variation within the two H. lanatus ecotypes could be investigated. At harvest at 7 weeks, roots and shoots were washed thoroughly with deionized water, separated, frozen in liquid nitrogen and stored at -80C until RNA extraction. RNA Extraction, QA and RNAseq: RNA extraction of frozen root tissue: Root samples were partly pre-ground, whilst cooling with liquid nitrogen, by hand in 1.5ml microcentrifuge tubes with 106m acid washed glass beads (Sigma-Aldrich) using disposable pestles (Sigma Aldrich), before processing in FastPrep tubes containing Lysing Matrix A on the Precellys 24-Dual using the same conditions as for shoots. RNA was extracted using an RNeasy Plant Mini Kit (QIAGEN), according to protocol and with inclusion of a DNA digestion step (DNase Set, QIAGEN) with the following amendment: 450l Buffer RLT (containing 4.5l -Mercaptoethanol) was added to the Precellys lysing tube containing the ground tissue and homogenised again using the Precellys 24-Dual for 5 seconds at 5500rpm to ensure that the powdered sample was suspended as quickly as possible to prevent RNA degradation. The lysate was transferred to a QIAshredder spin column and centrifuged at 14,000rpm for 2 minutes, followed by RNA extraction according to the standard protocoll. RNA was then eluted twice using the same eluate to further concentrate the RNA and stored at -80 C. RNA was quantified using a Nanodrop 8000 spectrophotometer (Thermo Scientific) and Agilent 2200 Tapestation (Agilent Technologies) to assess quality (purity and integrity) of the RNA. 21/23 root samples passed the QA and were submitted for RNAseq (all three hydroponics root samples passed, but 3 roots samples from the soil experiment failed the QC and could therefore not be processed for library preparation for the RNAseq study, hence there are 4 replicates for 3 treatments and 5 replicates for 1 treatment. Transcriptome sequencing (Illumina, RNAseq) was conducted at the Genome Analysis Centre (TGAC), Norwich, UK. Barcoded 125bp paired end TruSeq RNA libraries (polyA selected) were generated for each RNA sample and sequenced on the Illumina HiSeq 2500.

text: acid

text: D

characteristic: genotype

text: lime quarry soil

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 28


E-MTAB-4014:Sample 29

status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Queen's University Belfast

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-4014:Sample 29

tag: Namespace:Queen's University Belfast

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: velvet grass

characteristic: common name

characteristic: description

text: acid

characteristic: ecotype

text: A

text: lime quarry soil

characteristic: growth condition

text: Holcus lanatus

characteristic: organism

text: Holcus lanatus

text: root

characteristic: organism part

text: Holcus lanatus

text: Sample 29

characteristic: title


E-MTAB-4014:Sample 3

text: Queen's University Belfast

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-4014:Sample 3

text: ArrayExpress

text: velvet grass

text: Protocols: Plant and soil collection: H. lanatus plants and topsoil were collected from three locations: 6 plants (6 lime genotypes) were selected from a disused limestone quarry soil (pH 7.5) in County Antrim, NI, hereafter referred to as lime, 6 plants (6 acid genotypes) from an acidic peat bog (pH 3.5) in County Tyrone, NI, hereafter referred to as acid, and 6 plants (6 intermediate genotypes) from an acid mineral rough grassland (pH 5.5) (County Down, NI), hereafter refereed to as intermediate. In each case plants were carefully selected within each habitat, with all plants at least 5m apart, so that each of the 6 plants represents a clone for a unique genotype of that particular habitat. Tillers from each plant were trans-planted into John Innes no. 2 compost to nutritionally neutralize all plants. Tillers from compost grown lime and acid ecotypes (5 genotypes each) were subsequently used for set up of a full factorial soil transplant experiment. Tillers from one genotype of each the acid, lime and intermediate population were subsequently grown in hydroponics for additional root acid stress relevant transcriptome sequencing data. Full factorial reciprocal soil transplant experiment: Tillers from 5 genotypes of each the acid and lime ecotype were transplanted from compost onto acid bog soil (total 10 pots) and grown in the growth chamber for 7 weeks. Replication was at the level of ecotype by using 5 tillers from 5 different clonal plants from each ecotype (5 genotypes per ecotype) rather than using multiple tillers from one plant, to ensure that natural variation within the two H. lanatus ecotypes could be investigated. At harvest at 7 weeks, roots and shoots were washed thoroughly with deionized water, separated, frozen in liquid nitrogen and stored at -80C until RNA extraction. RNA Extraction, QA and RNAseq: RNA extraction of frozen shoot tissue: Shoot samples were homogenized in FastPrep Lysing tubes containing Lysing Matrix D (MP Biomedicals, USA) using two 20-second Precellys 24-Dual (Bertin Technologies, France) runs at 5500rpm to produce a fine powder. Inbetween runs the tubes were submerged into liquid nitrogen to prevent degradation of RNA. RNA was extracted using an RNeasy Plant Mini Kit (QIAGEN), according to protocol and with inclusion of a DNA digestion step (DNase Set, QIAGEN) with the following amendment: 450l Buffer RLT (containing 4.5l -Mercaptoethanol) was added to the Precellys lysing tube containing the ground tissue and homogenised again using the Precellys 24-Dual for 5 seconds at 5500rpm to ensure that the powdered sample was suspended as quickly as possible to prevent RNA degradation. The lysate was transferred to a QIAshredder spin column and centrifuged at 14,000rpm for 2 minutes, followed by RNA extraction according to the standard protocoll. RNA was then eluted twice using the same eluate to further concentrate the RNA and stored at -80 C. RNA was quantified using a Nanodrop 8000 spectrophotometer (Thermo Scientific) and Agilent 2200 Tapestation (Agilent Technologies) to assess quality (purity and integrity) of the RNA. 19/20 shoot samples passed the QA and were submitted for RNAseq. 1 shoots sample from the soil experiment failed the QC and could therefore not be processed for library preparation for the RNAseq study, hence there are 5 replicates for 3 treatments and 4 replicates for 1 treatment. Transcriptome sequencing (Illumina, RNAseq) was conducted at the Genome Analysis Centre (TGAC), Norwich, UK. Barcoded 125bp paired end TruSeq RNA libraries (polyA selected) were generated for each RNA sample and sequenced on the Illumina HiSeq 2500.

text: acid

text: F

characteristic: genotype

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 3


E-MTAB-4014:Sample 30

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 30

text: ArrayExpress

text: velvet grass

text: acid

text: F

text: lime quarry soil

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 30


E-MTAB-4014:Sample 31

characteristic: External Id

text: Queen's University Belfast

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: E-MTAB-4014:Sample 31

text: ArrayExpress

text: velvet grass

text: acid

text: B

text: lime quarry soil

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 31


E-MTAB-4014:Sample 32

text: Queen's University Belfast

text: public

characteristic: SRA accession

text: E-MTAB-4014:Sample 32

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: velvet grass

text: acid

text: C

text: lime quarry soil

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 32


E-MTAB-4014:Sample 33

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 33

text: ArrayExpress

text: velvet grass

characteristic: common name

characteristic: description

text: lime

characteristic: ecotype

text: R

text: lime quarry soil

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 33


E-MTAB-4014:Sample 34

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 34

text: ArrayExpress

text: velvet grass

text: lime

text: O

text: lime quarry soil

characteristic: growth condition

text: Holcus lanatus

characteristic: organism

text: Holcus lanatus

text: root

characteristic: organism part

text: Holcus lanatus

text: Sample 34


E-MTAB-4014:Sample 35

text: Queen's University Belfast

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-4014:Sample 35

text: ArrayExpress

text: velvet grass

text: lime

text: I

text: lime quarry soil

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 35

characteristic: title


E-MTAB-4014:Sample 36

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 36

text: ArrayExpress

text: velvet grass

text: lime

text: H

characteristic: genotype

text: lime quarry soil

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 36


E-MTAB-4014:Sample 37

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Queen's University Belfast

characteristic: INSDC center name

text: public

text: E-MTAB-4014:Sample 37

text: ArrayExpress

text: velvet grass

text: Protocols: Plant and soil collection: H. lanatus plants and topsoil were collected from three locations: 6 plants (6 lime genotypes) were selected from a disused limestone quarry soil (pH 7.5) in County Antrim, NI, hereafter referred to as lime, 6 plants (6 acid genotypes) from an acidic peat bog (pH 3.5) in County Tyrone, NI, hereafter referred to as acid, and 6 plants (6 intermediate genotypes) from an acid mineral rough grassland (pH 5.5) (County Down, NI), hereafter refereed to as intermediate. In each case plants were carefully selected within each habitat, with all plants at least 5m apart, so that each of the 6 plants represents a clone for a unique genotype of that particular habitat. Tillers from each plant were trans-planted into John Innes no. 2 compost to nutritionally neutralize all plants. Tillers from compost grown lime and acid ecotypes (5 genotypes each) were subsequently used for set up of a full factorial soil transplant experiment. Tillers from one genotype of each the acid, lime and intermediate population were subsequently grown in hydroponics for additional root acid stress relevant transcriptome sequencing data. Plants grown in hydroponics for additional root RNA samples for meta-transcriptome assembly: To obtain some pure plant root RNA for generation of the meta-transcriptome assembly, relevant to acid stress, tillers of one individual from each of the acid and lime ecotype were transferred to 0.5mM CaCl2 solution to equilibrate for 10 days. Tillers were then transferred to 50M AlCl3 solution for 48 hours, followed by harvesting of roots for RNAseq. Roots were washed thoroughly with deionized water, separated, frozen in liquid nitrogen and stored at -80C until RNA extraction. RNA Extraction, QA and RNAseq: RNA extraction of frozen root tissue: Root samples were partly pre-ground, whilst cooling with liquid nitrogen, by hand in 1.5ml microcentrifuge tubes with 106m acid washed glass beads (Sigma-Aldrich) using disposable pestles (Sigma Aldrich), before processing in FastPrep tubes containing Lysing Matrix A on the Precellys 24-Dual using the same conditions as for shoots. RNA was extracted using an RNeasy Plant Mini Kit (QIAGEN), according to protocol and with inclusion of a DNA digestion step (DNase Set, QIAGEN) with the following amendment: 450l Buffer RLT (containing 4.5l -Mercaptoethanol) was added to the Precellys lysing tube containing the ground tissue and homogenised again using the Precellys 24-Dual for 5 seconds at 5500rpm to ensure that the powdered sample was suspended as quickly as possible to prevent RNA degradation. The lysate was transferred to a QIAshredder spin column and centrifuged at 14,000rpm for 2 minutes, followed by RNA extraction according to the standard protocoll. RNA was then eluted twice using the same eluate to further concentrate the RNA and stored at -80 C. RNA was quantified using a Nanodrop 8000 spectrophotometer (Thermo Scientific) and Agilent 2200 Tapestation (Agilent Technologies) to assess quality (purity and integrity) of the RNA. 21/23 root samples passed the QA and were submitted for RNAseq (all three hydroponics root samples passed, but 3 roots samples from the soil experiment failed the QC and could therefore not be processed for library preparation for the RNAseq study, hence there are 4 replicates for 3 treatments and 5 replicates for 1 treatment. Transcriptome sequencing (Illumina, RNAseq) was conducted at the Genome Analysis Centre (TGAC), Norwich, UK. Barcoded 125bp paired end TruSeq RNA libraries (polyA selected) were generated for each RNA sample and sequenced on the Illumina HiSeq 2500.

text: acid

text: hydroponics plus Al

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 37


E-MTAB-4014:Sample 38

text: Queen's University Belfast

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-4014:Sample 38

characteristic: Submitter Id

text: ArrayExpress

text: velvet grass

text: lime

text: hydroponics plus Al

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 38


E-MTAB-4014:Sample 39

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 39

text: ArrayExpress

characteristic: broker name

text: velvet grass

characteristic: common name

text: Protocols: Plant and soil collection: H. lanatus plants and topsoil were collected from three locations: 6 plants (6 lime genotypes) were selected from a disused limestone quarry soil (pH 7.5) in County Antrim, NI, hereafter referred to as lime, 6 plants (6 acid genotypes) from an acidic peat bog (pH 3.5) in County Tyrone, NI, hereafter referred to as acid, and 6 plants (6 intermediate genotypes) from an acid mineral rough grassland (pH 5.5) (County Down, NI), hereafter refereed to as intermediate. In each case plants were carefully selected within each habitat, with all plants at least 5m apart, so that each of the 6 plants represents a clone for a unique genotype of that particular habitat. Tillers from each plant were trans-planted into John Innes no. 2 compost to nutritionally neutralize all plants. Tillers from compost grown lime and acid ecotypes (5 genotypes each) were subsequently used for set up of a full factorial soil transplant experiment. Tillers from one genotype of each the acid, lime and intermediate population were subsequently grown in hydroponics for additional root acid stress relevant transcriptome sequencing data. Plants grown in hydroponics for additional root RNA samples for meta-transcriptome assembly: To obtain some pure plant root RNA for generation of the meta-transcriptome assembly, tillers of one individual from each of the intermediate ecotype were transferred to 0.5mM CaCl2 solution to equilibrate for 10 days. A tiller from one individual of the intermediate ecotype was transfered to fresh 5mM CaCl2 solution for 48 hours, followed by harvesting of roots for RNAseq. Roots were washed thoroughly with deionized water, separated, frozen in liquid nitrogen and stored at -80C until RNA extraction. RNA Extraction, QA and RNAseq: RNA extraction of frozen root tissue: Root samples were partly pre-ground, whilst cooling with liquid nitrogen, by hand in 1.5ml microcentrifuge tubes with 106m acid washed glass beads (Sigma-Aldrich) using disposable pestles (Sigma Aldrich), before processing in FastPrep tubes containing Lysing Matrix A on the Precellys 24-Dual using the same conditions as for shoots. RNA was extracted using an RNeasy Plant Mini Kit (QIAGEN), according to protocol and with inclusion of a DNA digestion step (DNase Set, QIAGEN) with the following amendment: 450l Buffer RLT (containing 4.5l -Mercaptoethanol) was added to the Precellys lysing tube containing the ground tissue and homogenised again using the Precellys 24-Dual for 5 seconds at 5500rpm to ensure that the powdered sample was suspended as quickly as possible to prevent RNA degradation. The lysate was transferred to a QIAshredder spin column and centrifuged at 14,000rpm for 2 minutes, followed by RNA extraction according to the standard protocoll. RNA was then eluted twice using the same eluate to further concentrate the RNA and stored at -80 C. RNA was quantified using a Nanodrop 8000 spectrophotometer (Thermo Scientific) and Agilent 2200 Tapestation (Agilent Technologies) to assess quality (purity and integrity) of the RNA. 21/23 root samples passed the QA and were submitted for RNAseq (all three hydroponics root samples passed, but 3 roots samples from the soil experiment failed the QC and could therefore not be processed for library preparation for the RNAseq study, hence there are 4 replicates for 3 treatments and 5 replicates for 1 treatment. Transcriptome sequencing (Illumina, RNAseq) was conducted at the Genome Analysis Centre (TGAC), Norwich, UK. Barcoded 125bp paired end TruSeq RNA libraries (polyA selected) were generated for each RNA sample and sequenced on the Illumina HiSeq 2500.

characteristic: description

text: intermediate

text: hydroponics

text: Holcus lanatus

text: Holcus lanatus

text: root

text: Holcus lanatus

text: Sample 39


E-MTAB-4014:Sample 4

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 4

text: ArrayExpress

text: velvet grass

text: acid

characteristic: ecotype

text: B

text: acid bog soil

characteristic: growth condition

text: Holcus lanatus

characteristic: organism

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 4


E-MTAB-4014:Sample 5

text: Queen's University Belfast

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-4014:Sample 5

text: ArrayExpress

text: velvet grass

text: acid

text: C

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

characteristic: organism part

text: Holcus lanatus

text: Sample 5


E-MTAB-4014:Sample 6

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 6

text: ArrayExpress

text: velvet grass

text: lime

text: K

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 6

characteristic: title


E-MTAB-4014:Sample 7

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 7

text: ArrayExpress

text: velvet grass

text: lime

text: R

characteristic: genotype

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 7


E-MTAB-4014:Sample 8

text: Queen's University Belfast

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-4014:Sample 8

text: ArrayExpress

text: velvet grass

text: lime

text: O

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 8


E-MTAB-4014:Sample 9

text: Queen's University Belfast

text: public

text: E-MTAB-4014:Sample 9

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: velvet grass

characteristic: common name

text: lime

text: I

text: acid bog soil

text: Holcus lanatus

text: Holcus lanatus

text: shoot

text: Holcus lanatus

text: Sample 9


text: Yeast

characteristic: ArrayExpress-Phenotype

text: Saccharomyces cerevisiae

characteristic: ArrayExpress-Species

text: SC

text: public

text: baker's yeast

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: INSDC first public

text: public

tag: Namespace:Institute of Biosciences and Medical Technology

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: VC-001 WBC


text: Institute of Biosciences and Medical Technology

characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-002 progression


characteristic: ENA-CHECKLIST

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-002 WBC


characteristic: ENA-FIRST-PUBLIC

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-005 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-007 WBC

characteristic: title


characteristic: ENA-LAST-UPDATE

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-008 progression


characteristic: External Id

text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-008 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-011 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-012 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-013 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-013 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-017 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-017 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-019 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-019 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-020 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-022 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-022 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-023 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-023 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-024 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-025 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-028 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-031 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-031 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-032 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-034 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-035 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-037 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-037 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-041 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-045 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-052 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-052 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-056 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-056 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-057 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-057 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-061 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-063 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-063 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-070 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-071 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-077 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-077 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-080 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-081 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-081 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-085 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-085 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-086 WBC


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-093 progression


text: public

text: human

text: Homo sapiens

text: Homo sapiens

text: VC-093 WBC


E-MTAB-4031:Sample 10

text: UCSF Diabetes Center

text: public

text: E-MTAB-4031:Sample 10

tag: Namespace:UCSF Diabetes Center

text: ArrayExpress

text: human

text: Protocols: Adipose tissue samples (100-150 mg) from the supraclavicular and abdominal areas were obtained using a suction adapted BergstrAsm needle, as previously described (Chondronikola et al., 2015). Approximately 100 mg of adipose tissue was used for extraction of RNA using a pure link RNA isolation mini kit (Life Technologies, Carlsbad). RNA quality (RIN: RNA Integrity Number) was determined by Bioanalyzer (Agilent Technologies) and samples with at least RIN of 5 were subjected to RNA-seq. Libraries were constructed as previously described (Nature Medicine 21, 389a394 (2015))

characteristic: description

text: Subject 2 MC 17 TN WAT

characteristic: individual

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E-MTAB-4031:Sample 7

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E-MTAB-4031:Sample 8

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text: ArrayExpress

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E-MTAB-4031:Sample 9

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text: ArrayExpress

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text: ChIP library from human neurons

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text: cultured neurons

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text: Gut

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characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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text: EMBL

text: public

text: human

text: Read files from sample K_18

text: Gut

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text: Faecal sample

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characteristic: geographic location (latitude)

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text: human-gut

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characteristic: ENA-LAST-UPDATE

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text: human

text: Read files from sample K_19

text: Gut

text: Faecal sample

text: Faecal sample

text: Finland

text: human-gut

text: metagenome

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characteristic: organism

text: Child gut microbiome under antibiotics

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text: Illumina HiSeq


characteristic: ENA-CHECKLIST

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text: EMBL

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characteristic: collection date

text: human

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text: Read files from sample K_2

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text: Finland

characteristic: geographic location (country and/or sea)

text: human-gut

text: metagenome

text: Homo sapiens

text: Child gut microbiome under antibiotics

text: Homo sapiens

text: Illumina HiSeq


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL

text: public

text: human

text: Read files from sample K_20

text: Gut

text: Faecal sample

text: Faecal sample

text: Finland

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

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text: Homo sapiens

text: Child gut microbiome under antibiotics

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characteristic: ENA-CHECKLIST

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text: EMBL

characteristic: INSDC center name

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text: public

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characteristic: Submitter Id

text: human

text: Read files from sample K_3

text: Gut

text: Faecal sample

text: Faecal sample

text: Finland

text: human-gut

text: metagenome

text: Homo sapiens

characteristic: organism

text: Child gut microbiome under antibiotics

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text: Illumina HiSeq


characteristic: ENA-LAST-UPDATE

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text: EMBL

text: public

characteristic: collection date

text: human

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text: Read files from sample K_4

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text: Faecal sample

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text: Finland

characteristic: geographic location (country and/or sea)

text: human-gut

text: metagenome

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text: Child gut microbiome under antibiotics

text: Homo sapiens

text: Illumina HiSeq


characteristic: ENA-CHECKLIST

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text: EMBL

text: public

text: human

text: Read files from sample K_5

text: Gut

text: Faecal sample

text: Faecal sample

text: Finland

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

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text: Homo sapiens

text: Child gut microbiome under antibiotics

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text: EMBL

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text: human

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text: Gut

text: Faecal sample

text: Faecal sample

text: Finland

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characteristic: organism

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text: Illumina HiSeq


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text: Homo sapiens

text: Illumina HiSeq


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text: EMBL

text: public

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text: Read files from sample K_8

text: Gut

text: Faecal sample

text: Faecal sample

text: Finland

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

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text: Homo sapiens

text: Child gut microbiome under antibiotics

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text: Homo sapiens

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characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

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text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Read files from sample K_9

text: Gut

text: Faecal sample

text: Faecal sample

text: Finland

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text: metagenome

text: Homo sapiens

characteristic: organism

text: Child gut microbiome under antibiotics

text: Homo sapiens

text: Illumina HiSeq


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Brown University

text: public

text: ena-SAMPLE-Brown University-09-11-2015-10:03:17:931-16

tag: Namespace:Brown University

text: fruit fly

characteristic: common name

text: Drosophila melanogaster

text: Drosophila melanogaster


name: E-MTAB-4035:1810027O10Rik knockout abdominal muscle bioreplicate 1

text: Functional Genomics EMBL-EBI

text: public

tag: Namespace:Functional Genomics EMBL-EBI

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Knockout mice were generated on C57BL/6N background as part of the Knockout Mouse Project as described in Skarnes et al. 2011. Nature 474(7351): 337-42. doi: 10.1038/nature10163 (for more information see www.mousephenotype.org; www.komp.org; or www.kompphenotype.org). Mice were euthanised at 16 weeks of age and liver, spleen, kidney, abdominal muscle , or gonadal adipose tissue was dissected for RNA extraction. The strains used in this study were 1810027O10Rik , Sik1, 3110043O21Rik, and 3110043O21Rik knockout mice. RNA extraction was performed 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 Library preparation was performed 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

characteristic: description

text: 1810027O10Rik knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: musculature

characteristic: organism part

text: abdomen

characteristic: sampling site

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


name: E-MTAB-4035:1810027O10Rik knockout abdominal muscle bioreplicate 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Functional Genomics EMBL-EBI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

text: 1810027O10Rik knockout

text: Mus musculus

text: Mus musculus

text: musculature

text: abdomen

text: Mus musculus

text: male

characteristic: title


name: E-MTAB-4035:1810027O10Rik knockout abdominal muscle bioreplicate 3

text: Functional Genomics EMBL-EBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: 1810027O10Rik knockout

text: Mus musculus

characteristic: organism

text: Mus musculus

text: musculature

text: abdomen

text: Mus musculus

text: male


name: E-MTAB-4035:1810027O10Rik knockout gonadal adipose bioreplicate 1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Functional Genomics EMBL-EBI

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: 1810027O10Rik knockout

text: Mus musculus

text: Mus musculus

text: adipose tissue

text: gonad

text: Mus musculus

text: male


name: E-MTAB-4035:1810027O10Rik knockout gonadal adipose bioreplicate 2

text: Functional Genomics EMBL-EBI

text: public

text: ArrayExpress

text: house mouse

characteristic: description

text: 1810027O10Rik knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: adipose tissue

characteristic: organism part

text: gonad

characteristic: sampling site

text: Mus musculus

text: male

characteristic: sex


name: E-MTAB-4035:1810027O10Rik knockout gonadal adipose bioreplicate 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Functional Genomics EMBL-EBI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

text: 1810027O10Rik knockout

text: Mus musculus

text: Mus musculus

text: adipose tissue

text: gonad

text: Mus musculus

text: male

characteristic: strain


name: E-MTAB-4035:1810027O10Rik knockout liver bioreplicate 1

text: Functional Genomics EMBL-EBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

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text: Mus musculus

text: liver

text: Mus musculus

text: male

characteristic: title


name: E-MTAB-4035:1810027O10Rik knockout liver bioreplicate 2

characteristic: ENA-LAST-UPDATE

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text: Functional Genomics EMBL-EBI

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: 1810027O10Rik knockout

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: male


name: E-MTAB-4035:1810027O10Rik knockout liver bioreplicate 3

text: Functional Genomics EMBL-EBI

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

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text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: male


name: E-MTAB-4035:1810027O10Rik knockout lung bioreplicate 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Functional Genomics EMBL-EBI

characteristic: INSDC center name

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characteristic: sex


name: E-MTAB-4035:1810027O10Rik knockout lung bioreplicate 2

text: Functional Genomics EMBL-EBI

characteristic: INSDC first public

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text: Mus musculus

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text: Mus musculus

text: male

characteristic: strain


name: E-MTAB-4035:1810027O10Rik knockout lung bioreplicate 3

characteristic: ENA-LAST-UPDATE

text: Functional Genomics EMBL-EBI

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: 1810027O10Rik knockout

text: Mus musculus

text: Mus musculus

text: lung

text: Mus musculus

text: male

characteristic: title


name: E-MTAB-4035:3110043O21Rik knockout kidney bioreplicate 1

characteristic: External Id

text: Functional Genomics EMBL-EBI

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: 3110043O21Rik knockout

text: Mus musculus

characteristic: organism

text: Mus musculus

text: kidney

text: Mus musculus

text: male


name: E-MTAB-4035:3110043O21Rik knockout kidney bioreplicate 2

text: Functional Genomics EMBL-EBI

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: 3110043O21Rik knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: kidney

characteristic: organism part

text: Mus musculus

text: male


name: E-MTAB-4035:3110043O21Rik knockout liver bioreplicate 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Functional Genomics EMBL-EBI

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

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text: Mus musculus

text: liver

text: Mus musculus

text: male

characteristic: sex


name: E-MTAB-4035:3110043O21Rik knockout liver bioreplicate 2

text: Functional Genomics EMBL-EBI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

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text: Mus musculus

text: liver

text: Mus musculus

text: male

characteristic: strain


name: E-MTAB-4035:3110043O21Rik knockout liver bioreplicate 3

characteristic: ENA-LAST-UPDATE

text: Functional Genomics EMBL-EBI

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: 3110043O21Rik knockout

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

characteristic: title


name: E-MTAB-4035:3110043O21Rik knockout spleen bioreplicate 1

characteristic: External Id

text: Functional Genomics EMBL-EBI

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: 3110043O21Rik knockout

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spleen

text: Mus musculus

text: male


name: E-MTAB-4035:3110043O21Rik knockout spleen bioreplicate 2

text: Functional Genomics EMBL-EBI

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: 3110043O21Rik knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: spleen

characteristic: organism part

text: Mus musculus

text: male


name: E-MTAB-4035:3110043O21Rik knockout spleen bioreplicate 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Functional Genomics EMBL-EBI

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

text: 3110043O21Rik knockout

text: Mus musculus

text: Mus musculus

text: spleen

text: Mus musculus

text: male

characteristic: sex


name: E-MTAB-4035:Sik1 knockout abdominal muscle bioreplicate 1

text: Functional Genomics EMBL-EBI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

text: Sik1 knockout

text: Mus musculus

text: Mus musculus

text: musculature

text: abdomen

characteristic: sampling site

text: Mus musculus

text: male

characteristic: strain


name: E-MTAB-4035:Sik1 knockout abdominal muscle bioreplicate 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Functional Genomics EMBL-EBI

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: Sik1 knockout

text: Mus musculus

text: Mus musculus

text: musculature

text: abdomen

text: Mus musculus

text: male

characteristic: title


name: E-MTAB-4035:Sik1 knockout abdominal muscle bioreplicate 3

text: Functional Genomics EMBL-EBI

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: Sik1 knockout

text: Mus musculus

characteristic: organism

text: Mus musculus

text: musculature

text: abdomen

text: Mus musculus

text: male


name: E-MTAB-4035:Sik1 knockout gonadal adipose bioreplicate 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Functional Genomics EMBL-EBI

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

text: Sik1 knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: adipose tissue

characteristic: organism part

text: gonad

text: Mus musculus

text: male


name: E-MTAB-4035:Sik1 knockout gonadal adipose bioreplicate 2

text: Functional Genomics EMBL-EBI

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characteristic: ENA-FIRST-PUBLIC

text: Functional Genomics EMBL-EBI

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

characteristic: description

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: spleen

text: Mus musculus

text: male


name: E-MTAB-4035:wild type genotype spleen bioreplicate 5

text: Functional Genomics EMBL-EBI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: spleen

text: Mus musculus

text: male

characteristic: sex


name: E-MTAB-4035:wild type genotype spleen bioreplicate 6

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Functional Genomics EMBL-EBI

text: public

text: ArrayExpress

text: house mouse

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: spleen

text: Mus musculus

text: male

characteristic: strain


name: E-MTAB-4035:wild type genotype spleen bioreplicate 7

text: Functional Genomics EMBL-EBI

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spleen

text: Mus musculus

text: male

characteristic: title


name: E-MTAB-4035:wild type genotype spleen bioreplicate 8

text: Functional Genomics EMBL-EBI

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: spleen

characteristic: organism part

text: Mus musculus

text: male


name: E-MTAB-4035:wild type genotype spleen bioreplicate 9

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Functional Genomics EMBL-EBI

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

characteristic: description

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: spleen

text: Mus musculus

text: male


text: Normal

characteristic: ArrayExpress-Phenotype

text: Mus musculus

characteristic: ArrayExpress-Species

text: MC20 1 -ve

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: Mus musculus

text: MC20 1 -ve


text: Infected

text: Mus musculus

text: MC20 2 +ve

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus

text: MC20 2 +ve

characteristic: strain


text: Normal

text: Mus musculus

text: MC24 1 -ve

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus

text: MC24 1 -ve


text: Infected

text: Mus musculus

text: MC24 2 +ve

characteristic: ENA-CHECKLIST

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: MC24 2 +ve


text: Normal

text: Mus musculus

text: MC28 1 -ve

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: MC28 1 -ve


text: Infected

text: Mus musculus

text: MC28 2 +ve

text: SC

characteristic: INSDC center name

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: MC28 2 +ve


E-MTAB-4034:BM_HSC_rep  1

text: public

text: E-MTAB-4034:BM_HSC_rep 1

tag: Namespace:Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven

text: 8 week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: hematopoietic stem cell

characteristic: cell type

text: house mouse

text: Protocols: Total adult bone marrow (ABM) cells were flushed from femurs and tibiae of male C57BL/6J mice, pooled, washed twice with phosphatebuffered saline (PBS; Gibco Invitrogen, CA) containing 0.1% bovine serum albumin (BSA; Sigma). Lineage negative cell isolation was performed using lineage cell depletion kit (Miltenyi Biotec, Germany). To isolate LT-HSCs from ABM, resulting Lin cells were stained with FITC conjugated antiSca1, PE conjugated antickit, APC conjugated antilineage antibody cocktail (BD Pharmingen, San Diego, CA), PerCP/Cy5.5 conjugated anti-CD150 and APC conjugated anti-CD48 antibodies. Cells were incubated on ice for 30 minutes. FL tissues were obtained from C57BL/6J embryos dissected at embryonic day (E) 14.5 (14 days after vaginal plug was observed). Ter-119 positive erythrocytes and erythrocyte progenitors were depleted using MACS columns (Miltenyi Biotec, Germany) and stained with Alexa Fluor 488 conjugated anti-lineage antibody cocktail (containing CD4, CD5, CD8a, CD45R, Ter-119, GR-1 antibodies), PE conjugated anti-CD11b, APC conjugated anti-Sca-1, PE-Cy7 conjugated anti-CD150 and Alexa Fluor 488 conjugated anti-CD48. Cells were incubated on ice for 30 minutes. After incubation of cells with antibodies, cells were washed once with PBS. HSCs were sorted by fluorescence-activated cell sorting (FACS), using a FACS ARIAIII (Becton Dickinson). HSCs were directly sorted in QIAzol lysis buffer from miRNeasy Micro Kit (QIAGEN) and stored at -80c until isolation. Fraction of cells were used to checked the purity which was >95 percent. Total RNA isolation was isolated from the indicated populations using miRNeasy Micro Kit (QIAGEN) according to the manufacturer's protocol. DNAse treatment was performed using RNAse-free DNAse Set (Qiagen). Total RNA from FL and BM HSC was amplified using Ovation RNA-seq V2 system (NuGen technologies, CA) as per manufacturers instructions. Amplified cDNA (1ug) was sheared using the Covaris system (Covaris, MA) and fragments of 200bp (180-220bp) selected to construct a cDNA library. The fragmented DNA is combined with End Repair Mix, incubate at 20C for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen),then add A-Tailing Mix, incubate at 37C for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20C for 15 min. Adapter-ligated DNA is selected by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are purified with Ampure XP Beads (AGENCOURT). The Qualified libraries will amplify on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3cBotHS,Illumina). And the amplified flowcell will be subjected to 2*90 bp paired-end sequencing on the HiSeq 2000 System (TruSeq SBS KIT-HS V3,Illumina).

characteristic: description

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: adult bone marrow

characteristic: organism part

text: lin- sca1+ ckit+ cd150+ cd48-

characteristic: phenotype

text: Mus musculus

text: BM_HSC_rep 1

characteristic: title


E-MTAB-4034:BM_HSC_rep  2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Inter-departmental Stem Cell Institute, KU Leuven, Belgium. Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-4034:BM_HSC_rep 2

text: 8 week

text: ArrayExpress

text: hematopoietic stem cell

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: adult bone marrow

text: lin- sca1+ ckit+ cd150+ cd48-

text: Mus musculus

text: BM_HSC_rep 2


E-MTAB-4034:FL_HSC_E14.5_rep 1

text: public

characteristic: SRA accession

text: E-MTAB-4034:FL_HSC_E14.5_rep 1

characteristic: Submitter Id

text: embryonic day 14.5

text: ArrayExpress

text: hematopoietic stem cell

text: house mouse

characteristic: common name

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: fetus

text: lin- sca1+ cd11b+ cd150+ cd48-

text: Mus musculus

characteristic: strain

text: FL_HSC_E14.5_rep 1


E-MTAB-4034:FL_HSC_E14.5_rep 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

text: public

text: E-MTAB-4034:FL_HSC_E14.5_rep 2

text: embryonic day 14.5

characteristic: age

text: ArrayExpress

characteristic: broker name

text: hematopoietic stem cell

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: fetus

text: lin- sca1+ cd11b+ cd150+ cd48-

text: Mus musculus

text: FL_HSC_E14.5_rep 2


E-MTAB-4038:Sample ESC

text: Shanghai Jiao Tong University

text: public

text: E-MTAB-4038:Sample ESC

tag: Namespace:Shanghai Jiao Tong University

text: ArrayExpress

characteristic: cell line

text: embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: Mouse FGSCs were maintained on 1% gelatin-coated dishes in minimum essential medium medium (MEM-), supplemented with 10% heat-inactivated fetal bovine serum (Gibco), 1 mM sodium pyruvate, 1 mM non-essential amino acids, 1 mM l-glutamine, 0.1 mM -mercaptoethanol (Sigma), 20 ng/ml LIF (Leukemia Inhibitory Factor, Peprotech), 10 ng/ml EGF (mouse epidermal growth factor; Peprotech), 10 ng/ml human GDNF (glial cell line-derived neurotrophic factor; Peprotech), 10 ng/ml human bFGF (basic fibroblast growth factor; Peprotech). The FGSC medium is steriled by filtration using 0.22m syring-driven filter unit (Millipore).And the medium was changed every 2 days and cells were subcultured using trypsin every 3 days at a 1:23 dilution. All cultures were maintained at 37 C in a 5% CO2 atmosphere. Mouse feeder free 129S4/SvJae ES cells were maintained on gelatin-coated dishes in Glasgow Minimum Essential medium (GMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum, 0.1mM -mercaptoethanol (GIBCO), 2 mM l-glutamine, 0.1 mM MEM non-essential amino acid, 5,000 units ml1 penicillin/streptomycin and 1,000 units ml1 of ESGRO (Chemicon) under feeder-free conditions. Total RNA of FGSC or ESC was extracted using TRIzol regent (Invitrogen) and resuspend in RNase free water. And 1ug total RNA was used to perform reverse transcription with Oligo-dT and random primer using SuperScript III reverse transcriptase(Invitrogen) Total RNA was extract with TRIzol Reagent . And 50 g total RNA was incubated with streptavidin dynabeads coated with biotinylated GsuI-oligo (dT) primer. The first strand cDNA was synthesized with SuperScript III (Invitrogen) and dNTP mix containing 5-methylated-dCTP instead of dCTP. Then the resulting DNA/RNA hybrids were treated with RNase H and DNA polymerase I before dsDNA was generated. Next, the resulting dsDNA was fragmentated to 200500 bp with fragmentase (NEB). 3terminal fragments were released from beads through Gsu I digestion, which were subjected to deep sequencing by Illumina HiSeq2000.

characteristic: description

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample ESC


E-MTAB-4038:Sample FGSC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Shanghai Jiao Tong University

text: public

text: E-MTAB-4038:Sample FGSC

text: ArrayExpress

text: female germline stem cell line

text: female germ line stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample FGSC

characteristic: title


characteristic: ArrayExpress-CellType

characteristic: ArrayExpress-Immunoprecipitate

text: Homo Sapien

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

characteristic: sample description

text: Homo sapiens


text: CTCF

text: Homo Sapien

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: Homo Sapien

text: SC

characteristic: INSDC center name

text: public

text: human

text: Homo sapiens

text: Homo sapiens


text: Input

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: Lin_neg_bone marrow

text: Mus musculus


text: UTX Bethyl Ab

text: female

text: Mus musculus

characteristic: External Id

text: SC

text: public

text: house mouse

text: Mus musculus

text: Lin_neg_bone marrow

text: Mus musculus


text: public

tag: Namespace:MAX PLANCK INSTITUTE FOR  EVOLUTIONARY BIOLOGY

text: eastern European house mouse

text: Whole Genome Resequencing from Mus musculus musculus Studenec, Czech Republic; wild population

characteristic: description

text: Mus musculus musculus

text: Mus musculus musculus

text: F

characteristic: sex

text: CR

characteristic: strain

text: Liver

characteristic: tissue type

text: WGS Mus musculus musculus Studenec, Czech Republic

characteristic: title


text: MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: eastern European house mouse

text: Whole Genome Resequencing from Mus musculus musculusAlmaty, Kazhakstan; wild population

text: Mus musculus musculus

text: Mus musculus musculus

text: F

text: AL

text: Liver

text: WGS Mus musculus musculus Almaty, Kazhakstan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: eastern European house mouse

text: Mus musculus musculus

text: Mus musculus musculus

text: M

text: AL

text: Liver


text: EMBL-EBI

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cells

text: zebrafish

text: EGFP-low

characteristic: condition

text: Protocols: A single kidney from heterozygote Tg(cd41:EGFP) or wild-type fish was dissected and carefully passed through a strainer using the plunger of a 1-mL syringe. In the follow up experiment, circulating GFP positive cells were collected from the dissected heart of the same fish. Cells were collected in cold 1xPBS/5% FBS. The kidney of a non-transgenic line was used to set up the gating and exclude autofluorescent cells. Dead cells were excluded based on propidium iodide (PI) staining. Individual cells were sorted, using a Becton Dickinson Influx sorter with 488- and 561 nm lasers 26, and collected in a single well of a 96 well plate containing 2.3 uL of 0.2 % Triton X-100 supplemented with 1 U/uL SUPERase In RNAse inhibitor (Ambion). At the same time, information about cell size and granularity, as well as the level of the fluorescence, were recorded. Whole transcriptome amplification and library preparation was performed using the Smart-seq2 protocol 27, 28, with ERCC spike-in controls added at the same time as the oligo-dT and dNTP mixture.

characteristic: egfp fluorescence

text: Original

characteristic: experiment

characteristic: fsc

text: Kidney

characteristic: location

text: Danio rerio

text: Danio rerio

characteristic: plate

text: Danio rerio

characteristic: ssc

characteristic: well


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL-EBI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: zebrafish

characteristic: common name

text: EGFP-low

characteristic: description

text: Original

text: Kidney

text: Danio rerio

characteristic: organism

text: Danio rerio

text: Danio rerio

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL-EBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cells

text: zebrafish

text: EGFP-high

text: Followup

text: Kidney

text: Danio rerio

text: Danio rerio

text: Danio rerio


text: EMBL-EBI

text: public

text: ArrayExpress

text: zebrafish

text: EGFP-low

characteristic: condition

characteristic: egfp fluorescence

text: Followup

characteristic: experiment

characteristic: fsc

text: Kidney

characteristic: location

text: Danio rerio

text: Danio rerio

characteristic: plate

text: Danio rerio

characteristic: ssc

characteristic: well


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL-EBI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: zebrafish

characteristic: common name

text: EGFP-low

characteristic: description

text: Followup

text: Kidney

text: Danio rerio

characteristic: organism

text: Danio rerio

text: Danio rerio

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL-EBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cells

text: zebrafish

text: EGFP-high

text: Followup

text: Kidney

text: Danio rerio

text: Danio rerio

text: Danio rerio


text: EMBL-EBI

text: public

text: ArrayExpress

text: zebrafish

text: EarlyEnriched

characteristic: condition

characteristic: egfp fluorescence

text: Followup

characteristic: experiment

characteristic: fsc

text: Kidney

characteristic: location

text: Danio rerio

text: Danio rerio

characteristic: plate

text: Danio rerio

characteristic: ssc

characteristic: well


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMBL-EBI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: zebrafish

characteristic: common name

text: EarlyEnriched

characteristic: description

text: Followup

text: Kidney

text: Danio rerio

characteristic: organism

text: Danio rerio

text: Danio rerio

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EMBL-EBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cells

text: zebrafish

text: EGFP-low

text: Followup

text: Circulation

text: Danio rerio

text: Danio rerio

text: Danio rerio