E-MTAB-4751:dhns1 spike

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: The Wadsworth Center

text: public

text: E-MTAB-4751:dhns1 spike

text: ArrayExpress

text: Protocols: E. coli MG1655 (WT or dhns::kanamycin) cultures were grown in duplicate at 37C in LB broth with 225 rpm shaking to an OD600 of 0.45-0.55. 1 mL of each culture was pelleted and stored at -20C for future RNA harvesting. An aliquot of each culture was also plated onto LB agar to quantify colony forming units (CFUs). Once CFUs were assessed, a Salmonella spike-in culture was grown at 37C in LB broth with 225 rpm shaking to an OD600 of 0.45-0.55. The Salmonella spike-in cells were washed once in 10 mL Tris Buffered Saline (TBS), and then re-suspended in 1 mL TBS. Based on the CFUs calculated for each E. coli sample, Salmonella cells were added so that they were exactly equal to 25% of the total amount of cells in each E. coli pellet. RNA was harvested from the spiked pellet using the hot phenol method. Hot phenol RNA prep: transfer 1mL of subculture to microcentrifuge tube. Spin 1mL at max speed for 1 min and remove supernatant. Resuspend in 0.4mL ethanol+5% acid phenol/chloroform, spin 1 min at max speed and remove supernatant. Resuspend in 1mL 1x TBS, spin 1 min at max speed and remove supernatant. Resuspend in 0.5mL RNA Lysis Buffer (2% SDS, 4mM EDTA) and boil samples for 3 min. Add 0.5mL acid phenol/chloroform to each tube and incubate for 6 min at 65 °C. Incubate 5 min on ice then spin tubes at max speed for 6 min. Transfer upper phase to phase lock tube, add equal volume (0.4mL) chloroform:isoamyl alcohol 24:1 and spin 6 min at max speed. Transfer upper phase to new phase lock tube, add equal volume (0.4mL) chloroform:isoamyl alcohol 24:1 and spin 6 min at max speed. Transfer upper phase to new tube containing 40uL 3M Na Acetate+2uL glycogen (20mg/mL stock). Add 1mL ice cold EtOH and precipitate at -20 °C overnight or 15min at -80 °C. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 15uL nuclease free water. DNase treat RNA - set up 50uL reaction including 8-10ug RNA, 5uL of 10X buffer and 1uL DNase enzyme (Ambion). Incubate 30 min at 37 °C. Stop reaction by adding 352uL DEPC H2O + 134uL acid phenol:chloroform + 268uL chloroform:isoamyl alcohol 24:1. Transfer all to phase lock tube and spin at max speed for 6 min. Transfer upper phase to new microcentrifuge tube containing 40uL 3M Na Acetate + 2uL glycogen (20mg/mL stock). Add 1mL ice cold EtOH and precipitate at -20 °C overnight or 15min at -80 °C. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 15uL nuclease free water. Remove ribosomal RNA using the RiboZero kit from EpiCentre - wash magnetic beads 2x in RNase free water, then resuspend in Resuspension Solution. Add 32.5uL beads to each tube then add 0.5uL RNase inhibitor. Mix together in final volume of 20uL: 2.5ug DNase treated RNA + 2uL Ribozero reaction buffer + 4uL Ribozero rRNA removal solution. Incubate at 68 °C for 10 min followed by RT for 5 min. Add RNA to beads, mix by pipetting and vortexing for 10 s. Incubate at RT for 5 min. Vortex for 5 s then incubate at 50 °C for 5 min. Place tubes on magnetic stand for 1 min and transfer RNA to new tube. Bring volume to 180uL with DEPC H2O, then add 18uL 3M Na Acetate + 2uL glycogen (20mg/mL stock). Add 0.6mL ice cold EtOH and precipitate at -20 °C overnight. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 8uL nuclease free water. Prepare libraries using EpiCentre ScriptSeq v2 kit following kit protocol. Fragment RNA and anneal cDNA synthesis primer in 12uL reaction containing nuclease free water + 40ng rRNA depleted RNA + 1uL RNA Fragmentation solution + 2uL cDNA Synthesis primer. Incubate at 85 °C for 5 min then place tubes on ice. Synthesize DNA by adding 3uL cDNA Synthesis Premix + 0.5uL 100mM DTT + 0.5uL StarScript Reverse Transcriptase. Incubate at 25 °C for 5 min then 42 °C for 20 min. Cool tubes to 37 °C. Add 1uL Finishing solution and incubate at 37 °C for 10 min then 95 °C for 3 min. Cool tubes to 25 °C then add 7.5uL Terminal Tagging Premix + 0.5uL DNA Polymerase to terminally tag the cDNA. Incubate at 25 °C for 15 min, 95 °C for 3 min, then cool to 4 °C. Purify the cDNA using the Qiagen MinElute PCR Purification Kit - Add 5V Buffer PB to sample and transfer all to MinElute column. Spin 1 min at max speed. Discard flow through. Add 0.75mL Buffer PE to column and spin 1 min at max speed. Discard flow through. Spin column for 1 min at max speed then transfer column to new tube. Add 23.4uL Buffer EB to column, incubate 1 min at room temp, then spin 1 min at max speed. Amplify library by setting up 50uL PCR using 22.5uL purified DNA. Add 25uL FailSafe PCR Premix E + 1uL Forward PCR primer + 1uL ScriptSeq Index PCR Primer + 0.5uL FailSafe PCR Enzyme (1.25U). Heat at 95 °C for 1 min, then 12 cycles of 95 °C for 30 sec, 55 °C for 30 sec and 68 °C for 3 min. Incubate at 68 °C for 7 minutes. Purify sample using AMPure XP Purification protocol. Add 50uL beads to each pcr sample. Mix by pipetting 10x. Transfer beads+sample to new tube and incubate at room temp for 15 min. Put tubes on magnetic stand for 5 min then remove supernatant. Wash beads 2x, each time with 0.2mL of 80% EtOH, let stand 1 min then remove supernatant. Air dry beads at room temp for 15 min. Add 12uL nuclease free water, remove tubes from magnetic stand and resuspend beads in water. Incubate at room temp for 2 min. Place tubes on magnetic stand for 5 min. Library is in supernatant. Transfer to new tube. Quantify using Qubit.

text: dhns::kanamycin

text: spiked with RNA from salmonella enterica subsp. enterica serovar typhimurium str. 14028 s

text: dhns1 spike


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: External Id

text: The Wadsworth Center

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:The Wadsworth Center

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Protocols: 2mL overnights were grown in LB 37C or 30C at 225rpm and then subcultured 1:100. At an OD 0.5-0.7, RNA was harvested using the hot phenol method. Hot phenol RNA prep: transfer 1mL of subculture to microcentrifuge tube. Spin 1mL at max speed for 1 min and remove supernatant. Resuspend in 0.4mL ethanol+5% acid phenol/chloroform, spin 1 min at max speed and remove supernatant. Resuspend in 1mL 1x TBS, spin 1 min at max speed and remove supernatant. Resuspend in 0.5mL RNA Lysis Buffer (2% SDS, 4mM EDTA) and boil samples for 3 min. Add 0.5mL acid phenol/chloroform to each tube and incubate for 6 min at 65 °C. Incubate 5 min on ice then spin tubes at max speed for 6 min. Transfer upper phase to phase lock tube, add equal volume (0.4mL) chloroform:isoamyl alcohol 24:1 and spin 6 min at max speed. Transfer upper phase to new phase lock tube, add equal volume (0.4mL) chloroform:isoamyl alcohol 24:1 and spin 6 min at max speed. Transfer upper phase to new tube containing 40uL 3M Na Acetate+2uL glycogen (20mg/mL stock). Add 1mL ice cold EtOH and precipitate at -20 °C overnight or 15min at -80 °C. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 15uL nuclease free water. DNase treat RNA - set up 50uL reaction including 8-10ug RNA, 5uL of 10X buffer and 1uL DNase enzyme (Ambion). Incubate 30 min at 37 °C. Stop reaction by adding 352uL DEPC H2O + 134uL acid phenol:chloroform + 268uL chloroform:isoamyl alcohol 24:1. Transfer all to phase lock tube and spin at max speed for 6 min. Transfer upper phase to new microcentrifuge tube containing 40uL 3M Na Acetate + 2uL glycogen (20mg/mL stock). Add 1mL ice cold EtOH and precipitate at -20 °C overnight or 15min at -80 °C. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 15uL nuclease free water. Remove ribosomal RNA using the RiboZero kit from EpiCentre - wash magnetic beads 2x in RNase free water, then resuspend in Resuspension Solution. Add 32.5uL beads to each tube then add 0.5uL RNase inhibitor. Mix together in final volume of 20uL: 2.5ug DNase treated RNA + 2uL Ribozero reaction buffer + 4uL Ribozero rRNA removal solution. Incubate at 68 °C for 10 min followed by RT for 5 min. Add RNA to beads, mix by pipetting and vortexing for 10 s. Incubate at RT for 5 min. Vortex for 5 s then incubate at 50 °C for 5 min. Place tubes on magnetic stand for 1 min and transfer RNA to new tube. Bring volume to 180uL with DEPC H2O, then add 18uL 3M Na Acetate + 2uL glycogen (20mg/mL stock). Add 0.6mL ice cold EtOH and precipitate at -20 °C overnight. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 8uL nuclease free water. Prepare libraries using EpiCentre ScriptSeq v2 kit following kit protocol. Fragment RNA and anneal cDNA synthesis primer in 12uL reaction containing nuclease free water + 40ng rRNA depleted RNA + 1uL RNA Fragmentation solution + 2uL cDNA Synthesis primer. Incubate at 85 °C for 5 min then place tubes on ice. Synthesize DNA by adding 3uL cDNA Synthesis Premix + 0.5uL 100mM DTT + 0.5uL StarScript Reverse Transcriptase. Incubate at 25 °C for 5 min then 42 °C for 20 min. Cool tubes to 37 °C. Add 1uL Finishing solution and incubate at 37 °C for 10 min then 95 °C for 3 min. Cool tubes to 25 °C then add 7.5uL Terminal Tagging Premix + 0.5uL DNA Polymerase to terminally tag the cDNA. Incubate at 25 °C for 15 min, 95 °C for 3 min, then cool to 4 °C. Purify the cDNA using the Qiagen MinElute PCR Purification Kit - Add 5V Buffer PB to sample and transfer all to MinElute column. Spin 1 min at max speed. Discard flow through. Add 0.75mL Buffer PE to column and spin 1 min at max speed. Discard flow through. Spin column for 1 min at max speed then transfer column to new tube. Add 23.4uL Buffer EB to column, incubate 1 min at room temp, then spin 1 min at max speed. Amplify library by setting up 50uL PCR using 22.5uL purified DNA. Add 25uL FailSafe PCR Premix E + 1uL Forward PCR primer + 1uL ScriptSeq Index PCR Primer + 0.5uL FailSafe PCR Enzyme (1.25U). Heat at 95 °C for 1 min, then 12 cycles of 95 °C for 30 sec, 55 °C for 30 sec and 68 °C for 3 min. Incubate at 68 °C for 7 minutes. Purify sample using AMPure XP Purification protocol. Add 50uL beads to each pcr sample. Mix by pipetting 10x. Transfer beads+sample to new tube and incubate at room temp for 15 min. Put tubes on magnetic stand for 5 min then remove supernatant. Wash beads 2x, each time with 0.2mL of 80% EtOH, let stand 1 min then remove supernatant. Air dry beads at room temp for 15 min. Add 12uL nuclease free water, remove tubes from magnetic stand and resuspend beads in water. Incubate at room temp for 2 min. Place tubes on magnetic stand for 5 min. Library is in supernatant. Transfer to new tube. Quantify using Qubit.

characteristic: description

text: dhns::kanamycin

characteristic: genotype

text: Escherichia coli str. K-12 substr. MG1655

characteristic: organism

text: not spiked with Salmonella RNA

characteristic: protocol

unit: Celsius

characteristic: temperature

characteristic: title

type: has member


E-MTAB-4751:dhns2 spike

characteristic: ENA-FIRST-PUBLIC

text: The Wadsworth Center

text: public

text: E-MTAB-4751:dhns2 spike

text: ArrayExpress

text: dhns::kanamycin

text: dhns2 spike


characteristic: ENA-LAST-UPDATE

text: The Wadsworth Center

text: public

text: ArrayExpress

text: wild type genotype

text: not spiked with Salmonella RNA


E-MTAB-4751:WT1 spike

characteristic: ENA-CHECKLIST

text: The Wadsworth Center

text: public

text: E-MTAB-4751:WT1 spike

text: ArrayExpress

text: wild type genotype

text: WT1 spike


E-MTAB-4751:WT2 spike

characteristic: External Id

text: The Wadsworth Center

text: public

text: E-MTAB-4751:WT2 spike

text: ArrayExpress

text: wild type genotype

text: WT2 spike


Exp1 Ctrl3

characteristic: INSDC center name

text: public

text: Exp1 Ctrl3

tag: Namespace:Institut de recherche experimentale et clinique - IREC

text: feces

characteristic: bio material

text: house mouse

characteristic: common name

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: Exp1 Ctrl3


Exp1 Ctrl4

text: Institut de recherche experimentale et clinique - IREC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Exp1 Ctrl4

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ctrl4


Exp1 Ctrl5

text: public

text: Exp1 Ctrl5

characteristic: Submitter Id

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ctrl5


Exp1 Ag46ppb 1

text: public

text: Exp1 Ag46ppb 1

text: feces

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Exp1 Ag46ppb 1


Exp1 Ag46ppb 2

text: public

text: Exp1 Ag46ppb 2

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag46ppb 2


Exp1 Ag46ppb 3

text: public

text: Exp1 Ag46ppb 3

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag46ppb 3


Exp1 Ag46ppb 4

text: public

text: Exp1 Ag46ppb 4

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag46ppb 4


Exp1 Ag460ppb 1

text: public

text: Exp1 Ag460ppb 1

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag460ppb 1


Exp1 Ag460ppb 2

text: public

text: Exp1 Ag460ppb 2

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag460ppb 2


Exp1 Ag460ppb 3

text: public

text: Exp1 Ag460ppb 3

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag460ppb 3


Exp1 Ag460ppb 4

text: public

text: Exp1 Ag460ppb 4

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag460ppb 4


Exp1 Ag460ppb 5

text: public

text: Exp1 Ag460ppb 5

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag460ppb 5


Exp1 Ag4600ppb 1

text: public

text: Exp1 Ag4600ppb 1

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag4600ppb 1


Exp1 Ag4600ppb 2

text: public

text: Exp1 Ag4600ppb 2

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag4600ppb 2


Exp1 Ag4600ppb 3

text: public

text: Exp1 Ag4600ppb 3

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag4600ppb 3


Exp1 Ag4600ppb 4

text: public

text: Exp1 Ag4600ppb 4

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag4600ppb 4


Exp1 Ag4600ppb 5

text: public

text: Exp1 Ag4600ppb 5

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag4600ppb 5


Exp1 Ag46ppb 5

text: public

text: Exp1 Ag46ppb 5

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp1 Ag46ppb 5


text: Salk Institute for Biological Studies

text: public

tag: Namespace:Salk Institute for Biological Studies

text: ArrayExpress

characteristic: broker name

text: Hippocampal Neural Progenitor Cell

characteristic: cell type

text: Norway rat

text: Protocols: AHNs were cultured in DMEM/F12 with N2 supplements and FGF2 Total RNA was extracted by RNAbee Illumina TruSeq single end library preparation

characteristic: description

text: adult

characteristic: developmental stage

text: Rattus norvegicus

text: Rattus norvegicus

text: control for miR-19 knockdown

characteristic: rna interference

text: Rattus norvegicus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Salk Institute for Biological Studies

text: public

text: ArrayExpress

text: Hippocampal Neural Progenitor Cell

text: Norway rat

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: knockdown of miR-19

text: Rattus norvegicus

characteristic: title


characteristic: External Id

text: Salk Institute for Biological Studies

characteristic: INSDC center name

text: public

text: ArrayExpress

text: Hippocampal Neural Progenitor Cell

text: Norway rat

characteristic: common name

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: overexpression of miR-19

text: Rattus norvegicus


text: Salk Institute for Biological Studies

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: Hippocampal Neural Progenitor Cell

text: Norway rat

text: adult

text: Rattus norvegicus

text: Rattus norvegicus

text: control for miR-19 overexpresssion

text: Rattus norvegicus


text: Sallk Institute for Biological Studies

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Sallk Institute for Biological Studies

text: ArrayExpress

text: human embryonic stem cell-derived hippocampal progenitor cell

text: human

text: Protocols: Hues 6 hES derived NPCs Illumina TruSeq stranded mRNA sample prep kit

text: PWRN2 knockdown

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Sallk Institute for Biological Studies

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

text: Scramble control

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


text: Sallk Institute for Biological Studies

text: public

text: ArrayExpress

text: single cell

characteristic: cell type

text: human

text: Protocols: post-mortem tissue collection multiple displacement amplification Illumina library preparation for whole genome sequencing

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: hippocampus

characteristic: organism part

text: NeuN positive staining

characteristic: phenotype

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Sallk Institute for Biological Studies

text: public

text: ArrayExpress

text: single cell

text: human

text: Homo sapiens

text: Homo sapiens

text: hippocampus

text: NeuN negative staining

text: Homo sapiens


characteristic: External Id

text: ANIMAL AND PLANT HEALTH AGENCY

characteristic: INSDC center name

text: public

tag: Namespace:ANIMAL AND PLANT HEALTH AGENCY

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Horse

characteristic: host

text: Staphylococcus aureus

text: Staphylococcus aureus

characteristic: spa type

text: LA-MRSA CC398

characteristic: title


text: ANIMAL AND PLANT HEALTH AGENCY

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: United Kingdom

text: Pig

text: Staphylococcus aureus

text: Staphylococcus aureus

text: LA-MRSA CC398


text: ANIMAL AND PLANT HEALTH AGENCY

text: public

characteristic: Submitter Id

text: United Kingdom

text: Bovine

text: Staphylococcus aureus

characteristic: organism

text: Staphylococcus aureus

text: LA-MRSA CC398


text: The University of Nottingham

text: public

tag: Namespace:The University of Nottingham

text: Aegilops sharonensis accession 2170001

characteristic: cultivar

text: Aegilops sharonensis 4Ssh translocation line in wheat

characteristic: description

text: Aegilops sharonensis

text: Aegilops sharonensis

text: leaf

characteristic: tissue type

text: Aegilops sharonensis 4Ssh segment


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The University of Nottingham

text: public

text: Aegilops sharonensis accession 2170001

text: Chinese Spring 4B(4Ssh) wheat substitution line

text: Aegilops sharonensis

text: Aegilops sharonensis

text: leaf

text: Aegilops sharonensis 4Ssh segment


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The University of Nottingham

text: public

text: Aegilops sharonensis accession 2170001

text: EMS-mutagenised Aegilops sharonensis 4Ssh translocation line in wheat

text: Aegilops sharonensis

text: Aegilops sharonensis

text: leaf

text: Aegilops sharonensis 4Ssh segment


Chinese Spring

text: The University of Nottingham

characteristic: INSDC center name

text: public

text: Chinese Spring

text: bread wheat

characteristic: common name

text: Chinese Spring CS94

text: Chinese Spring wheat

text: Triticum aestivum

text: Triticum aestivum

text: leaf

text: Chinese Spring wheat


text: UNIVERSITY OF FREIBURG

text: public

tag: Namespace:UNIVERSITY OF FREIBURG

text: house mouse

text: DNA of P1 cardiomyocytes_Rep1

text: Mus musculus

text: Mus musculus


text: UNIVERSITY OF FREIBURG

text: public

text: house mouse

text: DNA of P1 cardiomyocytes_Rep2

text: Mus musculus

text: Mus musculus


text: UNIVERSITY OF FREIBURG

text: public

text: house mouse

text: DNA of P1 cardiomyocytes_rep3

text: Mus musculus

text: Mus musculus


text: CHINA ACADEMY

text: public

tag: Namespace:CHINA ACADEMY

text: rice

text: Oryza sativa

text: Oryza sativa

text: rice-sample


text: SAMRC Centre for Tuberculosis Research

text: public

tag: Namespace:SAMRC Centre for Tuberculosis Research

characteristic: collection date

text: South Africa

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: Mycobacterium tuberculosis

characteristic: isolate

text: Sputum

characteristic: isolation source

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis clinical isolates from South Africa


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University

characteristic: Submitter Id

text: Wastewater

characteristic: environment (biome)

text: Sequencing batch reactor

characteristic: environment (feature)

text: Activated sludge

characteristic: environment (material)

text: Denmark

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Propionivibrio sp. S1

text: Genome assembly of EBPR organisms

characteristic: project name

text: Propionivibrio sp. S1

text: Illumina

characteristic: sequencing method

text: Activated sludge SBR

characteristic: title

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University

characteristic: INSDC center name

text: public

characteristic: collection date

text: Wastewater

text: Sequencing batch reactor

text: Activated sludge

text: Denmark

characteristic: geographic location (country and/or sea)

text: metagenome

text: Candidatus Accumulibacter sp. S1

characteristic: organism

text: Genomes for EBPR organisms

text: Candidatus Accumulibacter sp. S1

text: Illumina

text: Lab scale SBR

text: wastewater/sludge


text: OXFORD

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Protocols: 37 centigrade continuous Qiagen RNA extraction kit

characteristic: description

text: bloodstream form

characteristic: developmental stage

text: 37 centigrade continuous

characteristic: growth condition

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei


characteristic: ENA-CHECKLIST

text: OXFORD

text: public

text: ArrayExpress

text: Protocols: 28 centigrade continuous Qiagen RNA extraction kit

text: procyclic form

text: 28 centigrade continuous

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

text: public

text: ArrayExpress

text: Protocols: 37 centigrade 24 hours Qiagen RNA extraction kit

text: procyclic form

text: 37 centigrade 24 hours

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei


characteristic: External Id

text: OXFORD

characteristic: INSDC center name

text: public

text: ArrayExpress

text: Protocols: 37 centigrade 48 hours Qiagen RNA extraction kit

text: procyclic form

text: 37 centigrade 48 hours

text: Trypanosoma brucei

text: Trypanosoma brucei

text: Trypanosoma brucei


text: UNIVERSITY OF OSLO

text: public

tag: Namespace:UNIVERSITY OF OSLO

text: yellowfin tuna

characteristic: common name

text: Thunnus albacares

text: Thunnus albacares

text: Global yellowfin tuna population samples.


text: FUBB

text: public

characteristic: collection date

text: wood

characteristic: environment (biome)

text: wood

characteristic: environment (feature)

text: wood

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: metagenome

characteristic: organism

text: Diversity and functionality of wood-tar degrading microbial consortia

characteristic: project name

text: metagenome

text: pyrosequencing

characteristic: sequencing method

text: Bacterial dinamics of wood-tar biodegradation


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CEAB

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: air

characteristic: air environmental package

text: atmosphere

text: aerosol

text: air

unit: m

characteristic: geographic location (altitude)

text: Spain

text: metagenome

text: air metagenome

text: Seasonal recurrence of airborne microbial communities

text: air metagenome

text: MySeq

text: Airborne eukarya

characteristic: title


Brassica napus microbiota1

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute of Technology Carlow

characteristic: INSDC center name

text: public

text: Brassica napus microbiota1

tag: Namespace:Institute of Technology Carlow

characteristic: collection date

text: Plant

characteristic: environment (biome)

text: Soil

characteristic: environment (feature)

text: Plant and soil

characteristic: environment (material)

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: phyllosphere metagenome

text: Brassica napus microbiota

text: phyllosphere metagenome

text: Illumina MiSeq

text: Impact of conservation and conventional tillage practices on microbiota associated to winter oilseed rape under Irish agronomic conditions


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: PHE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Neonate; haemorrhagic

characteristic: description

text: Cerebral spinal fluid

characteristic: isolation site

text: Mycoplasma hominis

characteristic: organism

text: Mycoplasma hominis

characteristic: year isolated


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: PHE

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Isolate from outside C-section wound

text: Genitalia

text: Mycoplasma hominis

text: Mycoplasma hominis

characteristic: title


text: PHE

characteristic: INSDC center name

text: public

text: Renal transplant

text: Peritoneal fluid

text: Mycoplasma hominis

text: Mycoplasma hominis


text: PHE

text: public

text: Post-termination operation

text: Blood culture

text: Mycoplasma hominis

text: Mycoplasma hominis


text: PHE

text: public

text: Mycoplasma hominis

text: Mycoplasma hominis


text: PHE

text: public

text: Hepatitis C Virus infection

text: Genitalia

text: Mycoplasma hominis

text: Mycoplasma hominis


text: PHE

text: public

text: Cervical swab

text: Mycoplasma hominis

text: Mycoplasma hominis


text: PHE

text: public

text: Knee aspirate

text: Mycoplasma hominis

text: Mycoplasma hominis


text: PHE

text: public

text: Neonate; 25 weeks gestation

text: Endotracheal secretions

text: Mycoplasma hominis

text: Mycoplasma hominis


text: PHE

text: public

text: Neonate; respiratory distress syndrome; twin

text: Ear swab

text: Mycoplasma hominis

text: Mycoplasma hominis


text: PHE

text: public

text: Cerebral abscess

text: Mycoplasma hominis

text: Mycoplasma hominis


text: PHE

text: public

text: Renal transplant

text: Abdominal pus

text: Mycoplasma hominis

text: Mycoplasma hominis


text: PHE

text: public

text: Pelvic haematoma after hysterectomy

text: Pelvic aspirate

text: Mycoplasma hominis

text: Mycoplasma hominis


text: PHE

text: public

text: Cardiac failure

text: Pleural fluid

text: Mycoplasma hominis

text: Mycoplasma hominis


text: PHE

text: public

text: Post-operative; deep tissue infection and superficial irritation; spinal abscess; spinal curdle C5; scoliosis instrumentation

text: Spinal tissue

text: Mycoplasma hominis

text: Mycoplasma hominis


text: UPENN

text: public

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Human colon tissue, flash frozen in liquid nitrogen, was obtained from the Cooperative Human Tissue Network (CHTN). 0.41 g of human colon was ground in a liquid nitrogen-cooled mortar, with the resulting cells being fixed using a previously published protocol (Hughes et al., Nature genetics, 2014). For both 4C and CaptureC methods, the initial 3C libraries were generated following a previously published protocol (Hughes et al., Nature genetics, 2014). For each of the HCT116-WT, HCT116-DEL and NCM460 libraries, 10 million cells were harvested and fixed. The DNA was digested using DpnII, then re-ligated together using T4 DNA ligase, and finally isolated by phenol/chloroform extraction. For the rest of the 4C method we followed another previously published protocol (van de Werken et al., Nature methods, 2012). We used NlaIII as the second restriction enzyme to digest the DNA followed by T4 ligation. PCR primers were designed with Illumina adaptors to flank the region harboring rs7903146 near DpnII and NlaIII cut sites. PCR and Illumina libraries were generated as previously described (van de Werken et al., Nature methods, 2012) with the exception of using a PCR annealing temperature of 55 C. Following the previously published captureC protocol (Hughes et al., Nature genetics, 2014) we utilized the above described 3C libraries for the capture procedure. The 3C libraries were sonicated to an average size of 200bp, ligated to Illumina adaptors, and amplified for 6 cycles with index primers to generate Illumina libraries. 140bp biotinylated DNA oligo probes were designed to each DpnII cut site flanking rs7903146 and were used in the two sequential pull downs of the capture libraries.

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: colon

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UPENN

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: 'The human colorectal cancer cell line, HCT116 (ATCC), was maintained at 37 C with 5% CO2 incubation in Dulbecco''s modified Eagle''s medium (DMEM), supplemented with 10% fetal bovine serum (HyClone), 100 U/ml penicillin and 100 mg/ml streptomycin.' The CRISPR/Cas9 approach was utilized to delete a 1.4kb region harboring the SNP rs7903146. For both 4C and CaptureC methods, the initial 3C libraries were generated following a previously published protocol (Hughes et al., Nature genetics, 2014). For each of the HCT116-WT, HCT116-DEL and NCM460 libraries, 10 million cells were harvested and fixed. The DNA was digested using DpnII, then re-ligated together using T4 DNA ligase, and finally isolated by phenol/chloroform extraction. For the rest of the 4C method we followed another previously published protocol (van de Werken et al., Nature methods, 2012). We used NlaIII as the second restriction enzyme to digest the DNA followed by T4 ligation. PCR primers were designed with Illumina adaptors to flank the region harboring rs7903146 near DpnII and NlaIII cut sites. PCR and Illumina libraries were generated as previously described (van de Werken et al., Nature methods, 2012) with the exception of using a PCR annealing temperature of 55 C. Following the previously published captureC protocol (Hughes et al., Nature genetics, 2014) we utilized the above described 3C libraries for the capture procedure. The 3C libraries were sonicated to an average size of 200bp, ligated to Illumina adaptors, and amplified for 6 cycles with index primers to generate Illumina libraries. 140bp biotinylated DNA oligo probes were designed to each DpnII cut site flanking rs7903146 and were used in the two sequential pull downs of the capture libraries.

text: CRISPR/Cas9-mediated deletion

characteristic: genetic modification

text: 1.4kb deletion in region of SNP rs7903146

text: Homo sapiens

text: Homo sapiens

text: colon

text: Homo sapiens


text: UPENN

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: Protocols: 'The human colorectal cancer cell line, HCT116 (ATCC), was maintained at 37 C with 5% CO2 incubation in Dulbecco''s modified Eagle''s medium (DMEM), supplemented with 10% fetal bovine serum (HyClone), 100 U/ml penicillin and 100 mg/ml streptomycin.' For both 4C and CaptureC methods, the initial 3C libraries were generated following a previously published protocol (Hughes et al., Nature genetics, 2014). For each of the HCT116-WT, HCT116-DEL and NCM460 libraries, 10 million cells were harvested and fixed. The DNA was digested using DpnII, then re-ligated together using T4 DNA ligase, and finally isolated by phenol/chloroform extraction. For the rest of the 4C method we followed another previously published protocol (van de Werken et al., Nature methods, 2012). We used NlaIII as the second restriction enzyme to digest the DNA followed by T4 ligation. PCR primers were designed with Illumina adaptors to flank the region harboring rs7903146 near DpnII and NlaIII cut sites. PCR and Illumina libraries were generated as previously described (van de Werken et al., Nature methods, 2012) with the exception of using a PCR annealing temperature of 55 C. Following the previously published captureC protocol (Hughes et al., Nature genetics, 2014) we utilized the above described 3C libraries for the capture procedure. The 3C libraries were sonicated to an average size of 200bp, ligated to Illumina adaptors, and amplified for 6 cycles with index primers to generate Illumina libraries. 140bp biotinylated DNA oligo probes were designed to each DpnII cut site flanking rs7903146 and were used in the two sequential pull downs of the capture libraries.

characteristic: description

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: colon

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UPENN

text: public

characteristic: INSDC status

text: ArrayExpress

text: human

text: Protocols: 'The NCM460 cells were purchased from INCELL Corporation, LLC and maintained in M3 medium according to the manufacturer''s protocol.' For both 4C and CaptureC methods, the initial 3C libraries were generated following a previously published protocol (Hughes et al., Nature genetics, 2014). For each of the HCT116-WT, HCT116-DEL and NCM460 libraries, 10 million cells were harvested and fixed. The DNA was digested using DpnII, then re-ligated together using T4 DNA ligase, and finally isolated by phenol/chloroform extraction. For the rest of the 4C method we followed another previously published protocol (van de Werken et al., Nature methods, 2012). We used NlaIII as the second restriction enzyme to digest the DNA followed by T4 ligation. PCR primers were designed with Illumina adaptors to flank the region harboring rs7903146 near DpnII and NlaIII cut sites. PCR and Illumina libraries were generated as previously described (van de Werken et al., Nature methods, 2012) with the exception of using a PCR annealing temperature of 55 C. Following the previously published captureC protocol (Hughes et al., Nature genetics, 2014) we utilized the above described 3C libraries for the capture procedure. The 3C libraries were sonicated to an average size of 200bp, ligated to Illumina adaptors, and amplified for 6 cycles with index primers to generate Illumina libraries. 140bp biotinylated DNA oligo probes were designed to each DpnII cut site flanking rs7903146 and were used in the two sequential pull downs of the capture libraries.

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: colon

text: Homo sapiens


text: NIOO-KNAW

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

characteristic: depth

text: Tropical and subtropical moist broadleaf forest biome

characteristic: environment (biome)

text: forest

characteristic: environment (feature)

text: rhizosphere

characteristic: environment (material)

text: Brazil

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: metagenome

text: Common bean rhizosphere microbiome

characteristic: project name

text: metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NIOO-KNAW

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: description

text: forest

text: bulk soil

text: Brazil

text: mimarks-survey

text: metagenome

characteristic: organism

text: Common bean rhizosphere microbiome

text: metagenome

text: Illumina

text: soil


text: NIOO-KNAW

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

characteristic: depth

text: terrestrial biome

characteristic: environment (biome)

text: agriculture

characteristic: environment (feature)

text: rhizosphere

characteristic: environment (material)

text: Brazil

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: mimarks-survey

text: metagenome

text: Common bean rhizosphere microbiome

text: metagenome

text: Illumina

text: soil


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NIOO-KNAW

text: public

text: terrestrial biome

text: agriculture

text: bulk soil

text: Brazil

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: metagenome

text: Common bean rhizosphere microbiome

characteristic: project name

text: metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

characteristic: title


text: Astatotilapia tweddlei

characteristic: ArrayExpress-Species

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: Astatotilapia tweddlei

characteristic: common name

text: Haplochromis tweddlei

characteristic: organism

text: Haplochromis tweddlei


text: Astatotilapia bloyeti

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Bloyet's haplo

text: Haplochromis bloyeti

text: Haplochromis bloyeti


text: Serranochromis robustus

characteristic: External Id

text: SC

text: public

text: Serranochromis robustus

text: Serranochromis robustus

text: Serranochromis robustus


text: Serranochromis angusticeps

text: SC

text: public

text: thinface cichlid

text: Serranochromis angusticeps

text: Serranochromis angusticeps


text: Pharyngochromis acuticeps

text: SC

text: public

text: Pharyngochromis acuticeps

text: Pharyngochromis acuticeps

text: Pharyngochromis acuticeps


text: Ctenochromis pectoralis

text: SC

text: public

text: Ctenochromis pectoralis

text: Ctenochromis pectoralis

text: Ctenochromis pectoralis


text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Lin_neg_bone marrow

characteristic: sample description

text: Mus musculus


text: female

text: Mus musculus

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


text: BAYLOR COLLEGE OF ME

text: public

tag: Namespace:BAYLOR COLLEGE OF ME

text: Escherichia coli K-12

text: Escherichia coli K-12

text: ChIPSeq samples


text: UNIVERSITY HOHENHEIM

text: public

tag: Namespace:UNIVERSITY HOHENHEIM

text: pig gut metagenome

text: pig gut metagenome

text: Sample


text: public

tag: Namespace:INSERM U944/CNRS UMR7212 Universite Paris Diderot

text: ArrayExpress

characteristic: broker name

text: Fibroblast

characteristic: cell type

text: human

text: Protocols: Skin biopsy Genomic DNA extracted from fibroblast cells with QIAGEN QIAamp DNA Mini Kit SureSelect Human All Exon Kits Version 5-UTRs

characteristic: description

text: Fanconi anemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: female

characteristic: sex


rice1 1

text: CHINA ACADEMY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: rice1 1

text: rice

text: Oryza sativa

text: Oryza sativa

characteristic: title


text: CNRS UMR 5088

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:CNRS UMR 5088

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: DIvA (AsiSI-ER-U20S)cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with antibiotics, 10% FCS (Invitrogen) and 1 μg/mL puromycin (DIvA cells) at 37 °C under a humidified atmosphere with 5% CO2. Capture Hi-C library generation was carried out as described previously 2. Briefly, 30.106 cells were fixed in 2% formaldehyde for 10 minutes. After overnight digestion with HindIII, DNA ends were labeled with biotin-14-dATP using the klenow fragment of DNA pol I and religated in preserved nuclei. 50 ug of DNA was sheared to an average size of 450 bp (Covaris). Sheared DNA was then end repaired, adenine tailed and double size selected from 250 to 600 bp (AMPure XP beads). Chimerae marked by biotin were pulled down using MyOne Streptavidin C1 DynaBeads (Invitrogen) and ligated to PE adaptors (Illumina). The Hi-C libraries (retained on the beads) were amplified using PE primers (Illumina) with 10 PCR amplification cycles. Capture was next carried out on Hi-C library, with SureSelect target enrichment, using the custom-designed biotinylated RNA bait library and custom paired-end blockers according to the manufacturer's instructions (Agilent Technologies). After library enrichment by capture, a post-capture PCR amplification step was carried out using PE PCR 1.0 and PE PCR 2.0 primers with 7 PCR amplification cycles. Captured-Hi-C libraries were performed on damaged (4OHT treated) or undamaged (untreated) samples in biological duplicates (BR#1 and BR#2) and were sequenced on the Illumina HiSeq 1000 platform.

text: damaged DNA

characteristic: genetic modification

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CNRS UMR 5088

text: public

text: ArrayExpress

text: human

text: Protocols: DIvA (AsiSI-ER-U20S)cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with antibiotics, 10% FCS (Invitrogen) and 1 μg/mL puromycin (DIvA cells) at 37 °C under a humidified atmosphere with 5% CO2. For AsiSI-dependent DSB induction, cells were treated with 300 nM 4OHT (Sigma, H7904) for 4 h. Capture Hi-C library generation was carried out as described previously 2. Briefly, 30.106 cells were fixed in 2% formaldehyde for 10 minutes. After overnight digestion with HindIII, DNA ends were labeled with biotin-14-dATP using the klenow fragment of DNA pol I and religated in preserved nuclei. 50 ug of DNA was sheared to an average size of 450 bp (Covaris). Sheared DNA was then end repaired, adenine tailed and double size selected from 250 to 600 bp (AMPure XP beads). Chimerae marked by biotin were pulled down using MyOne Streptavidin C1 DynaBeads (Invitrogen) and ligated to PE adaptors (Illumina). The Hi-C libraries (retained on the beads) were amplified using PE primers (Illumina) with 10 PCR amplification cycles. Capture was next carried out on Hi-C library, with SureSelect target enrichment, using the custom-designed biotinylated RNA bait library and custom paired-end blockers according to the manufacturer's instructions (Agilent Technologies). After library enrichment by capture, a post-capture PCR amplification step was carried out using PE PCR 1.0 and PE PCR 2.0 primers with 7 PCR amplification cycles. Captured-Hi-C libraries were performed on damaged (4OHT treated) or undamaged (untreated) samples in biological duplicates (BR#1 and BR#2) and were sequenced on the Illumina HiSeq 1000 platform.

text: undamaged DNA

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens


Exp2 Ctrl1

text: Institut de recherche experimentale et clinique - IREC

text: public

text: Exp2 Ctrl1

text: feces

characteristic: bio material

text: house mouse

text: Mus musculus

text: Mus musculus

characteristic: strain

text: Exp2 Ctrl1


Exp2 Ctrl2

text: public

text: Exp2 Ctrl2

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp2 Ctrl2


Exp2 Ctrl3

text: public

text: Exp2 Ctrl3

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp2 Ctrl3


Exp2 Ag46ppb 1

text: public

text: Exp2 Ag46ppb 1

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp2 Ag46ppb 1


Exp2 Ag46ppb 2

text: public

text: Exp2 Ag46ppb 2

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp2 Ag46ppb 2


Exp2 Ag46ppb 3

text: public

text: Exp2 Ag46ppb 3

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp2 Ag46ppb 3


Exp2 Ag460ppb 1

text: public

text: Exp2 Ag460ppb 1

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp2 Ag460ppb 1


Exp2 Ag460ppb 2

text: public

text: Exp2 Ag460ppb 2

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp2 Ag460ppb 2


Exp2 Ag460ppb 3

text: public

text: Exp2 Ag460ppb 3

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp2 Ag460ppb 3


Exp2 Ag4600ppb 1

text: public

text: Exp2 Ag4600ppb 1

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp2 Ag4600ppb 1


Exp2 Ag4600ppb 2

text: public

text: Exp2 Ag4600ppb 2

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp2 Ag4600ppb 2


Exp2 Ag4600ppb 3

text: public

text: Exp2 Ag4600ppb 3

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp2 Ag4600ppb 3


text: Homo sapiens

characteristic: ArrayExpress-Species

text: SC

text: public

text: human

text: Homo sapiens

text: Homo sapiens


Exp3 Ctrl1

characteristic: INSDC center name

text: public

text: Exp3 Ctrl1

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ctrl1


Exp3 Ctrl2

characteristic: INSDC first public

text: public

text: Exp3 Ctrl2

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ctrl2


Exp3 Ctrl3

characteristic: INSDC last update

text: public

text: Exp3 Ctrl3

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ctrl3


Exp3 Ctrl4

text: public

text: Exp3 Ctrl4

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ctrl4

characteristic: title


Exp3 Ag46ppb 1

text: public

characteristic: INSDC status

text: Exp3 Ag46ppb 1

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ag46ppb 1


Exp3 Ag46ppb 2

text: public

characteristic: SRA accession

text: Exp3 Ag46ppb 2

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Effect of Ag NP on gut microbiota - Exp3


Exp3 Ag46ppb 3

text: public

text: Exp3 Ag46ppb 3

characteristic: Submitter Id

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ag46ppb 2


Exp3 Ag46ppb 4

text: public

text: Exp3 Ag46ppb 4

text: feces

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: Exp3 Ag46ppb 4


Exp3 Ag46ppb 5

text: public

text: Exp3 Ag46ppb 5

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ag46ppb 5


Exp3 Ag460ppb 1

text: public

text: Exp3 Ag460ppb 1

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ag460ppb 1


Exp3 Ag460ppb 2

text: public

text: Exp3 Ag460ppb 2

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ag460ppb 2


Exp3 Ag460ppb 3

text: public

text: Exp3 Ag460ppb 3

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ag460ppb 3


Exp3 Ag460ppb 4

text: public

text: Exp3 Ag460ppb 4

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ag460ppb 4


Exp3 Ag460ppb 5

text: public

text: Exp3 Ag460ppb 5

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ag460ppb 5


Exp3 Ag4600ppb 1

text: public

text: Exp3 Ag4600ppb 1

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ag4600ppb 1


Exp3 Ag4600ppb 2

text: public

text: Exp3 Ag4600ppb 2

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ag4600ppb 2


Exp3 Ag4600ppb 3

text: public

text: Exp3 Ag4600ppb 3

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ag4600ppb 3


Exp3 Ag4600ppb 4

text: public

text: Exp3 Ag4600ppb 4

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ag4600ppb 4


Exp3 Ag4600ppb 5

text: public

text: Exp3 Ag4600ppb 5

text: feces

text: house mouse

text: Mus musculus

text: Mus musculus

text: Exp3 Ag4600ppb 5


text: Blood

characteristic: ArrayExpress-CellType

text: Blood

characteristic: ArrayExpress-OrganismPart

text: male

characteristic: ArrayExpress-Sex

text: Homo sapiens

text: SC

text: public

text: human

text: Homo sapiens

text: RNA

characteristic: sample description

text: Homo sapiens


text: male

text: Homo sapiens

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: human

text: Homo sapiens

text: RNA

text: Homo sapiens


text: FUBB

text: public

characteristic: collection date

text: Soil

characteristic: environment (biome)

text: Soil

characteristic: environment (feature)

text: Soil

characteristic: environment (material)

text: Italy

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: metagenome

characteristic: organism

text: Diversity and functionality of wood-tar degrading microbial consortia

characteristic: project name

text: metagenome

text: pyrosequencing

characteristic: sequencing method

text: Fungi associated with tar


text: Chinese Hamster

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

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: Chinese Hamster

characteristic: common name

text: Cricetulus griseus

text: genomic DNA

characteristic: sample description

text: Cricetulus griseus

characteristic: strain

text: Cricetinae

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRA (INRA Toulouse)

text: public

tag: Namespace:INRA (INRA Toulouse)

text: sheep

text: breed with a short and woolly coat

characteristic: description

text: Ovis aries

text: Ovis aries


text: INRA (INRA Toulouse)

text: public

text: sheep

text: one of the QTL ram of the Romane experimental protocol

text: Ovis aries

characteristic: organism

text: Ovis aries


text: INRA (INRA Toulouse)

text: public

text: sheep

text: breed with a long and hairy coat

text: Ovis aries

text: Ovis aries


text: GENETIC DIVERSITY CENTRE

text: public

tag: Namespace:GENETIC DIVERSITY CENTRE

text: Silene latifolia

text: Silene latifolia

text: male

characteristic: sex

text: flower buds without calyxes

characteristic: tissue type


text: QMUL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: European ash

text: Fraxinus excelsior

text: Fraxinus excelsior


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: UNIVERSITY OF CAMBRIDGE

text: public

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF CAMBRIDGE

characteristic: Submitter Id

characteristic: collection date

characteristic: depth

text: Boreal

characteristic: environment (biome)

text: Lake

characteristic: environment (feature)

text: Sediment

characteristic: environment (material)

text: Canada

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

characteristic: miscellaneous parameter

characteristic: o2 consumption

text: freshwater sediment metagenome

text: Daisy Lake Shotgun

characteristic: project name

characteristic: respiration rate

text: freshwater sediment metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina

characteristic: sequencing method

text: Daisy Lake shotgun


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BAYLOR COLLEGE OF ME

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Escherichia coli K-12

characteristic: organism

text: Escherichia coli K-12

text: WGS samples

characteristic: title


siteJ _DSB_WGS1

text: BAYLOR COLLEGE OF ME

text: public

text: siteJ _DSB_WGS1

text: Escherichia coli K-12

text: Escherichia coli K-12

text: WGS samples


siteJ _DSB_WGS2

text: BAYLOR COLLEGE OF ME

text: public

text: siteJ _DSB_WGS2

text: Escherichia coli K-12

text: Escherichia coli K-12

text: WGS samples


siteJ _DSB_recA_WGS1

text: BAYLOR COLLEGE OF ME

text: public

text: siteJ _DSB_recA_WGS1

text: Escherichia coli K-12

text: Escherichia coli K-12

text: WGS samples


siteJ _DSB_recA_WGS2

text: BAYLOR COLLEGE OF ME

text: public

text: siteJ _DSB_recA_WGS2

text: Escherichia coli K-12

text: Escherichia coli K-12

text: WGS samples


siteJ _DSB_recB_WGS1

text: BAYLOR COLLEGE OF ME

text: public

text: siteJ _DSB_recB_WGS1

text: Escherichia coli K-12

text: Escherichia coli K-12

text: WGS samples


siteJ _DSB_recB_WGS2

text: BAYLOR COLLEGE OF ME

text: public

text: siteJ _DSB_recB_WGS2

text: Escherichia coli K-12

text: Escherichia coli K-12

text: WGS samples


siteJ _DSB_recF_WGS1

text: BAYLOR COLLEGE OF ME

text: public

text: siteJ _DSB_recF_WGS1

text: Escherichia coli K-12

text: Escherichia coli K-12

text: WGS samples


siteJ _DSB_recF_WGS2

text: BAYLOR COLLEGE OF ME

text: public

text: siteJ _DSB_recF_WGS2

text: Escherichia coli K-12

text: Escherichia coli K-12

text: WGS samples


siteJ _DSB_ruvA_WGS1

text: BAYLOR COLLEGE OF ME

text: public

text: siteJ _DSB_ruvA_WGS1

text: Escherichia coli K-12

text: Escherichia coli K-12

text: WGS samples


siteJ _DSB_ruvA_WGS2

text: BAYLOR COLLEGE OF ME

text: public

text: siteJ _DSB_ruvA_WGS2

text: Escherichia coli K-12

text: Escherichia coli K-12

text: WGS samples


text: 445 N Fifth St

text: public

tag: Namespace:445 N Fifth St

characteristic: collection date

text: human

characteristic: common name

text: Temperate Forest

characteristic: environment (biome)

text: city

characteristic: environment (feature)

text: human

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Homo sapiens

text: Homo sapiens

text: Illumina 450k


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Technical University of Denmark

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Technical University of Denmark

text: Sputum metagenomic reads alligned to PAO1 (GenBank accession NC_002516.2; genome size of 6.4 Mb) with Bowtie 2 V2.0.2 and The Genome Analysis Toolkit (GATK) V1.0.5083 for realignment around indels. Removing all non-P. aeruginosa reads from the metagenomic reads. The pileups of read alignments were performed with SAM tools V0.1.7 (r50), and the uploded data is the .bam files.

characteristic: description

text: Denmark

text: Human

characteristic: host scientific name

text: Sputum sample S1

characteristic: isolate

text: Sputum sample

characteristic: isolation source

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: P. aeruginosa population from sputum sample


text: Technical University of Denmark

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Denmark

text: Human

text: Sputum sample S2

text: Sputum sample

text: Pseudomonas aeruginosa

characteristic: organism

text: Pseudomonas aeruginosa

characteristic: title


characteristic: ENA-CHECKLIST

text: Technical University of Denmark

text: public

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

text: Sputum sample S3

text: Sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Technical University of Denmark

text: public

text: Denmark

text: Human

text: Sputum sample S4a

text: Sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


characteristic: External Id

text: Technical University of Denmark

characteristic: INSDC center name

text: public

text: Denmark

text: Human

text: Sputum sample S4b

text: Sputum sample

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: Streptococcus pneumoniae

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC first public

text: public

text: Streptococcus pneumoniae

characteristic: common name

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: JHI

text: public

text: barley

text: Developing grain, bracts removed (5 DPA), replicate 2, batch 2

characteristic: description

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

characteristic: INSDC last update

text: public

text: barley

text: Developing grain, bracts removed (5 DPA), replicate 3, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

characteristic: INSDC status

text: barley

text: Developing grain, bracts removed (5 DPA), replicate 4, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

characteristic: SRA accession

text: barley

text: 4-day embryos dissected from germinating grains, replicate A, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

characteristic: Submitter Id

text: barley

text: 4-day embryos dissected from germinating grains, replicate B, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: 4-day embryos dissected from germinating grains, replicate C, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Roots from the seedlings (10 cm shoot stage), replicate A, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Roots from the seedlings (10 cm shoot stage), replicate B, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Roots from the seedlings (10 cm shoot stage), replicate C, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing grain, bracts removed (15 DPA), replicate 1, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing grain, bracts removed (15 DPA), replicate 2, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing grain, bracts removed (15 DPA), replicate 4, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Shoots from the seedlings (10 cm shoot stage), replicate A, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Shoots from the seedlings (10 cm shoot stage), replicate B, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Shoots from the seedlings (10 cm shoot stage), replicate C, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing inflorescences (1-1.5 cm), replicate F, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing inflorescences (1-1.5 cm), replicate G, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing inflorescences (1-1.5 cm), replicate H, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing tillers at six leaf stage, 3rd internode, replicate A, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing tillers at six leaf stage, 3rd internode, replicate B, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing tillers at six leaf stage, 3rd internode, replicate C, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Young developing inflorescences (5mm), replicate A, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Young developing inflorescences (5mm), replicate B, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Young developing inflorescences (5mm), replicate c, batch 2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing grain, bracts removed (5 DPA), replicate 2, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing grain, bracts removed (5 DPA), replicate 3, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing grain, bracts removed (5 DPA), replicate 4, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: 4-day embryos dissected from germinating grains, replicate A, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: 4-day embryos dissected from germinating grains, replicate B, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: 4-day embryos dissected from germinating grains, replicate C, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Roots from the seedlings (10 cm shoot stage), replicate A, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Roots from the seedlings (10 cm shoot stage), replicate B, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Roots from the seedlings (10 cm shoot stage), replicate C, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing grain, bracts removed (15 DPA), replicate 1, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing grain, bracts removed (15 DPA), replicate 2, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing grain, bracts removed (15 DPA), replicate 4, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Shoots from the seedlings (10 cm shoot stage), replicate A, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Shoots from the seedlings (10 cm shoot stage), replicate B, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Shoots from the seedlings (10 cm shoot stage), replicate C, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing inflorescences (1-1.5 cm), replicate F, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing inflorescences (1-1.5 cm), replicate G, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing inflorescences (1-1.5 cm), replicate H, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing tillers at six leaf stage, 3rd internode, replicate A, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing tillers at six leaf stage, 3rd internode, replicate B, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Developing tillers at six leaf stage, 3rd internode, replicate C, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Young developing inflorescences (5mm), replicate A, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Young developing inflorescences (5mm), replicate B, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Young developing inflorescences (5mm), replicate c, batch 1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Etiolated (10 day old seedling), replicate1, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Etiolated (10 day old seedling), replicate2, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Etiolated (10 day old seedling), replicate3, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Lemma (6 weeks PA), replicate1, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Lemma (6 weeks PA), replicate2, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Lemma (6 weeks PA), replicate3, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Lodicule (6 weeks PA), replicate1, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Lodicule (6 weeks PA), replicate2, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Lodicule (6 weeks PA), replicate3, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Palea (6 weeks PA), replicate1, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Palea (6 weeks PA), replicate2, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Palea (6 weeks PA), replicate3, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Epidermis (4 weeks ), replicate1, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Epidermis (4 weeks ), replicate2, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Epidermis (4 weeks ), replicate3, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Rachis (5 weeks PA), replicate1, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Rachis (5 weeks PA), replicate2, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Rachis (5 weeks PA), replicate3, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Root (4 weeks ), replicate1, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Root (4 weeks ), replicate2, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Root (4 weeks ), replicate3, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Senescing leaf (2months), replicate1, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Senescing leaf (2months), replicate2, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Senescing leaf (2months), replicate3, batch1

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Etiolated (10 day old seedling), replicate1, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Etiolated (10 day old seedling), replicate2, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Etiolated (10 day old seedling), replicate3, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Lemma (6 weeks PA), replicate1, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Lemma (6 weeks PA), replicate2, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Lemma (6 weeks PA), replicate3, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Lodicule (6 weeks PA), replicate1, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Lodicule (6 weeks PA), replicate2, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Lodicule (6 weeks PA), replicate3, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Palea (6 weeks PA), replicate1, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Palea (6 weeks PA), replicate2, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Palea (6 weeks PA), replicate3, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Epidermis (4 weeks ), replicate1, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Epidermis (4 weeks ), replicate2, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Epidermis (4 weeks ), replicate3, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Rachis (5 weeks PA), replicate1, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Rachis (5 weeks PA), replicate2, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Rachis (5 weeks PA), replicate3, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Root (4 weeks ), replicate1, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Root (4 weeks ), replicate2, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Root (4 weeks ), replicate3, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Senescing leaf (2months), replicate1, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Senescing leaf (2months), replicate2, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: Senescing leaf (2months), replicate3, batch2

text: Hordeum vulgare

text: Hordeum vulgare


text: JHI

text: public

text: barley

text: barley cultivar, exome captured

text: Hordeum vulgare

text: Hordeum vulgare


E-MTAB-4786:Sample 1

text: University College London (UCL)

text: public

text: E-MTAB-4786:Sample 1

tag: Namespace:University College London (UCL)

text: ArrayExpress

characteristic: broker name

text: CD8 single positive thymocytes

characteristic: cell type

text: house mouse

text: Protocols: Cell sorting by FACS 0hr vs 4hr PBS stimulation vs 4hr TNF (30ng/mL) stimulation RNA converted to cDNA RNA isolation Preparation of a cDNA library for sequencing

text: F5 Rag1-/-

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: strain

text: Sample 1


E-MTAB-4786:Sample 10

characteristic: ENA-CHECKLIST

text: University College London (UCL)

text: public

text: E-MTAB-4786:Sample 10

text: ArrayExpress

text: CD8 single positive thymocytes

text: house mouse

text: F5 Rag1-/-

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Tumor Necrosis Factor

characteristic: stimulus

text: Sample 10

characteristic: title


E-MTAB-4786:Sample 11

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University College London (UCL)

characteristic: INSDC center name

text: public

text: E-MTAB-4786:Sample 11

text: ArrayExpress

text: CD8 single positive thymocytes

text: house mouse

text: F5 Rag1-/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Tumor Necrosis Factor

text: Sample 11


E-MTAB-4786:Sample 2

text: University College London (UCL)

characteristic: INSDC first public

text: public

text: E-MTAB-4786:Sample 2

text: ArrayExpress

text: CD8 single positive thymocytes

text: house mouse

characteristic: common name

characteristic: description

text: F5 Rag1-/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 2


E-MTAB-4786:Sample 3

text: University College London (UCL)

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-4786:Sample 3

text: ArrayExpress

text: CD8 single positive thymocytes

text: house mouse

text: F5 Rag1-/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Sample 3


E-MTAB-4786:Sample 4

text: University College London (UCL)

text: public

text: E-MTAB-4786:Sample 4

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: CD8 single positive thymocytes

characteristic: cell type

text: house mouse

text: F5 Rag1-/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Phosphate-buffered saline

text: Sample 4


E-MTAB-4786:Sample 5

characteristic: ENA-CHECKLIST

text: University College London (UCL)

text: public

text: E-MTAB-4786:Sample 5

text: ArrayExpress

text: CD8 single positive thymocytes

text: house mouse

text: F5 Rag1-/-

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Phosphate-buffered saline

characteristic: strain

text: Sample 5


E-MTAB-4786:Sample 6

text: University College London (UCL)

text: public

text: E-MTAB-4786:Sample 6

text: ArrayExpress

text: CD8 single positive thymocytes

text: house mouse

text: F5 Rag1-/-

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Phosphate-buffered saline

characteristic: stimulus

text: Sample 6

characteristic: title


E-MTAB-4786:Sample 7

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University College London (UCL)

text: public

text: E-MTAB-4786:Sample 7

text: ArrayExpress

text: CD8 single positive thymocytes

text: house mouse

text: F5 Rag1-/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Phosphate-buffered saline

text: Sample 7


E-MTAB-4786:Sample 8

text: University College London (UCL)

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-4786:Sample 8

text: ArrayExpress

text: CD8 single positive thymocytes

text: house mouse

characteristic: common name

text: F5 Rag1-/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Tumor Necrosis Factor

text: Sample 8


E-MTAB-4786:Sample 9

text: University College London (UCL)

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-4786:Sample 9

text: ArrayExpress

text: CD8 single positive thymocytes

text: house mouse

characteristic: description

text: F5 Rag1-/-

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Tumor Necrosis Factor

text: Sample 9


text: MD ANDERSON CANCER CENTER

text: public

characteristic: SRA accession

tag: Namespace:MD ANDERSON CANCER CENTER

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens


text: Streptococcus pneumoniae

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: UCSDMI

text: public

characteristic: altitude

characteristic: anonymized name

text: False

text: metagenome

text: USA

characteristic: country

characteristic: depth

text: BLANK WH1 11H

text: True

characteristic: elevation

text: urban biome

characteristic: env biome

text: research facility

characteristic: env feature

text: sterile water

characteristic: env matter

text: misc environment

characteristic: env package

text: True

text: blank

characteristic: host common name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: metagenome

text: UC Davis

text: False

text: True

characteristic: public

text: completed

text: sterile water

characteristic: sample type

text: metagenome

text: Patterns of microbiome transition along salinity gradients, and importance for fish host adaptive divergence across osmotic boundaries.


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

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text: False

text: metagenome

characteristic: common name

text: USA

text: BLANK WH1 12A

characteristic: description

text: True

text: urban biome

text: research facility

text: sterile water

text: misc environment

text: True

text: blank

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characteristic: organism

text: UC Davis

text: False

text: True

text: completed

text: sterile water

text: metagenome

characteristic: title


text: UCSDMI

text: public

characteristic: altitude

characteristic: anonymized name

text: False

text: metagenome

text: USA

characteristic: country

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text: BLANK WH1 12B

text: True

characteristic: elevation

text: urban biome

characteristic: env biome

text: research facility

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text: sterile water

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text: True

text: blank

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characteristic: latitude

characteristic: longitude

text: metagenome

text: UC Davis

text: False

text: True

text: completed

text: sterile water

text: metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

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characteristic: SRA accession

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text: False

text: metagenome

characteristic: common name

text: USA

text: BLANK WH1 12C

characteristic: description

text: True

text: urban biome

text: research facility

text: sterile water

text: misc environment

text: True

text: blank

text: metagenome

text: UC Davis

text: False

text: True

characteristic: public

text: completed

text: sterile water

characteristic: sample type

text: metagenome


text: UCSDMI

text: public

characteristic: altitude

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text: False

text: metagenome

text: USA

characteristic: country

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text: BLANK WH1 12D

text: True

characteristic: elevation

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characteristic: env biome

text: research facility

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text: sterile water

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text: misc environment

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text: True

text: blank

characteristic: host common name

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text: metagenome

characteristic: organism

text: UC Davis

text: False

text: True

text: completed

text: sterile water

text: metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: False

text: metagenome

characteristic: common name

text: USA

text: BLANK WH1 12E

characteristic: description

text: True

text: urban biome

text: research facility

text: sterile water

text: misc environment

text: True

text: blank

characteristic: latitude

characteristic: longitude

text: metagenome

text: UC Davis

text: False

text: True

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text: metagenome


text: UCSDMI

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text: False

text: metagenome

text: USA

characteristic: country

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text: BLANK WH1 12F

text: True

characteristic: elevation

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text: True

text: blank

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text: UC Davis

text: False

text: True

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text: sterile water

characteristic: sample type

text: metagenome


characteristic: ENA-CHECKLIST

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characteristic: External Id

text: UCSDMI

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text: public

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text: False

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text: USA

text: BLANK WH1 12G

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text: True

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text: True

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text: False

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text: True

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characteristic: ENA-CHECKLIST

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characteristic: External Id

text: UCSDMI

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text: BLANK WH10 9A

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text: True

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text: True

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characteristic: ENA-CHECKLIST

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text: UCSDMI

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text: public

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text: False

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text: UCSDMI

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text: public

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