text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC first public

text: public

text: not provided

text: malaria parasite P. falciparum

characteristic: common name

text: not provided

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: title


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:European Centre for Disease Prevention and Control

characteristic: Submitter Id

text: National Public Health Organization (NPHO) in Greece

characteristic: collection date

text: Hospital-associated isolate of Klebsiella pneumoniae

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: European Centre for Disease Prevention and Control

text: public

text: Greece

text: Homo sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: Queen Mary University of London

characteristic: GAL

text: Tree of Life Programme

characteristic: INSDC first public

text: public

tag: Namespace:Tree of Life Programme

text: JEFF DRAZEN | ROBERT VRIJENHOEK

text: MONTEREY BAY AQUARIUM RESEARCH INSTITUTE | MONTEREY BAY AQUARIUM RESEARCH INSTITUTE

characteristic: collecting institution

unit: m

characteristic: depth

text: USA

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Pacific Ocean off northern California | Mendocino Ridge

characteristic: geographic location (region and locality)

text: cold seep

characteristic: habitat

text: GREG ROUSE | MARINA MCCOWIN

text: SCRIPPS INSTITUTION OF OCEANOGRAPHY AT THE UNIVERSITY OF CALIFORNIA SAN DIEGO | SCRIPPS INSTITUTION OF OCEANOGRAPHY AT THE UNIVERSITY OF CALIFORNIA SAN DIEGO

text: not collected

characteristic: lifestage

text: Chromatiales bacterium LBARH1

text: **OTHER SOMATIC ANIMAL TISSUE**

characteristic: organism part

text: ASG

characteristic: project name

characteristic: sample symbiont of

text: Chromatiales bacterium LBARH1

text: NOT COLLECTED

characteristic: sex

text: Y

characteristic: symbiont

characteristic: tolid


E-MTAB-13237:Trem1 +/+

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Post Doctoral Fellow

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13237:Trem1 +/+

tag: Namespace:Post Doctoral Fellow

characteristic: Submitter Id

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

text: Protocols: Mice Model: 8-week-old male mice were used in all experiments.Trem1 knockout mice on a C57BL/6 genetic background were generated as described in our previous report (Nguyen-Lefebvre AT, Ajith A, Portik-Dobos V, Horuzsko DD, Arbab AS, Dzutsev A, et al. The innate immune receptor TREM-1 promotes liver injury and fibrosis. J Clin Invest. 2018;128(11):4870-83). Breeding of Trem1 heterozygous parents (Trem1+/-) yielded Trem1-/- and Trem1+/+ offspring. PCR genotyping of offspring was performed based on the product sizes, 300 and 506 bp for the Trem1+/+ and mutant alleles, respectively. The ratio of Trem1-/-, Trem1+/- , and Trem1+/+ offspring did not deviate significantly from the expected 1:2:1 ratio. All animals were grossly normal, with normal weight and appearance. The expression of Trem1 was analyzed by PCR amplification of a 152-bp product using forward (5'-CGCCTGGTGGTGACCAAGGG-3') and reverse (5'-ACAACCGCAGTGGGCTTGGG-3') primers. Trem1+/+ littermate controls were used as the control for the in vivo tumorigenesis studies. Cell culture:The murine melanoma cell line B16-F10 (ATCC, cat. no. CRL-6475) was maintained in RPMI media (STEMCELL Technologies, cat. no. 36750) supplemented with 10% heat-inactivated FBS and penicillin-streptomycin. Tumor Model:8-week-old Trem1+/+ or Trem1-/- mice were subcutaneously injected with syngeneic 105 B16F10 murine melanoma cells. Mice were euthanized on the 22nd day post tumor cell injection. Freshly harvested tumors from Trem1+/+ or Trem1-/- mice were processed into a single-cell suspension using the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotech, cat. no. 130-096-427) in combination with the tumor dissociation kit (Miltenyi Biotech, cat. no. 130-095-929).Single-cell RNA sequencing sample preparation: Freshly harvested tumors from Trem1+/+ and Trem1-/- mice were pooled separately into 2 groups to maximize the isolation of tumor infiltrating myeloid cells. Tumors were gently dissociated using the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotech). Single-cell suspensions of tumor cells were purified by incubation with CD45(Miltenyi Biotec, cat. no. 130-110-618) Microbeads as per the manufacturer’s instructions to enrich the tumor-infiltrating cells. 7,000-8,000 live myeloid cells were loaded onto the Chromium Controller (10x Genomics), and scRNA-seq libraries were generated using Chromium Next GEM Single Cell 3’ Reagent kit v3.1 (10x Genomics) according to the manufacturer’s protocol. The libraries were sequenced on NextSeq 500 (Illumina) using Mid Output v2.5 (150 cycles) kit (Illumina) with 28 bp (Read 1), 8 bp (Indexing Run), and 91 bp (RNA Read 2) to collect approximately 23K mean reads per cell at the range of 1,294,379 median genes per cell. Reads from the raw fastq files were mapped to the mm10 mouse genome reference by STAR aligner linked with the Cell Ranger v5.0.1 pipeline to output clusters representing the cell populations and the upregulated genes annotated as the cell surface markers in each cell population. The output was imported into Loupe Browser v6.0 (10x Genomics) for visualization along with further analysis.Freshly harvested tumors from Trem1+/+ and Trem1-/- mice were pooled separately into 2 groups to maximize the isolation of tumor infiltrating myeloid cells. Tumors were gently dissociated using the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotech). Single-cell suspensions of tumor cells were purified by incubation with CD45, CD11b Microbeads (Miltenyi Biotec, cat. no. 130-049-601) as per the manufacturer’s instructions to enrich the tumor-infiltrating myeloid cells. Quality and quantity of cells were assessed under the microscope by trypan blue staining, and dead cells were removed using the Dead Cell Removal Kit (STEMCELL, cat. no. 17899) as per the manufacturer’s instructions. Nuclei acid extraction was performed following the manufacturer's instructions (10x Genomics, as part of the Chromium Single Cell 3' v3.1). Tocapture approximately 5,000 targeted cells, 7,000-8,000 live myeloid cells were loaded onto theChromium Controller (10x Genomics), and scRNA-seq libraries were generated using ChromiumNext GEM Single Cell 3’ Reagent kit v3.1 (10x Genomics) according to the manufacturer’sprotocol.

characteristic: description

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

characteristic: growth condition

text: mixed pool 1

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: skin

text: neoplasm

characteristic: sampling site

text: Mus musculus

text: male

characteristic: strain

text: Trem1 +/+

characteristic: title


E-MTAB-13237:Trem1 -/-

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Post Doctoral Fellow

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13237:Trem1 -/-

text: ArrayExpress

text: not collected

text: house mouse

text: Trem1 -/-

text: not collected

text: subcutaneously injected with syngeneic 105 B16F10 murine melanoma cells

text: mixed pool 2

text: not applicable

text: Mus musculus

text: Mus musculus

text: skin

characteristic: organism part

text: neoplasm

text: Mus musculus

text: male

characteristic: sex

text: Trem1 -/-


E-MTAB-13244:Sample 1

text: Petersburg Nuclear Physics Institute

text: public

characteristic: SRA accession

text: E-MTAB-13244:Sample 1

tag: Namespace:Petersburg Nuclear Physics Institute

characteristic: Submitter Id

text: 8 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

text: Protocols: Sixteen mice C57BL/6 8–12 weeks old weighing 22–26 g were generated and separated into four groups with four animals in each, and treated with the following solutions: 0.9% sodium chloride solution (vehicle mice), conduritol -epoxide (CBE) with MPTP (MPTP-CBE), CBE, MPTP. The brain samples were removed from the skull and cut along the midsagittal plane. The substantia nigra was dissected under a dissecting microscope with an ocular micrometer (Nikon SMZ660, Nikon, Melville, NY, USA). Total RNA was extracted from brain tissue with Trisol reagent and PureLink RNA micro Kit (PureLink RNA micro Kit, Invitrogen, CA, USA ), according to the manufactur-er’s instruction. PolyA RNA was purified with Dynabeads® mRNA Purification Kit (Dynabeads® mRNA Purification Kit, Ambion, TX, USA ). The Illumina library was made from polyA NEBNext® Ultra™ II RNA Library Prep (NEB-Next® Ultra™ II RNA Library Prep, NEB, MA, USA ), according to the manual.

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

text: Mus musculus

text: substantia nigra

text: Mus musculus

text: male

text: Sample 1


E-MTAB-13244:Sample 10

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Petersburg Nuclear Physics Institute

text: public

text: E-MTAB-13244:Sample 10

text: 8 to 12

text: ArrayExpress

text: not collected

text: house mouse

text: adult

text: wild type genotype

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: substantia nigra

text: Mus musculus

text: male

characteristic: strain

text: Sample 10

characteristic: title


E-MTAB-13244:Sample 11

text: Petersburg Nuclear Physics Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13244:Sample 11

characteristic: Submitter Id

text: 8 to 12

characteristic: age

text: ArrayExpress

text: not collected

text: house mouse

text: adult

text: wild type genotype

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: substantia nigra

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: Sample 11


E-MTAB-13244:Sample 12

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Petersburg Nuclear Physics Institute

text: public

text: E-MTAB-13244:Sample 12

text: 8 to 12

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

text: Mus musculus

text: substantia nigra

text: Mus musculus

text: male

text: Sample 12


E-MTAB-13244:Sample 13

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Petersburg Nuclear Physics Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13244:Sample 13

text: 8 to 12

text: ArrayExpress

text: not collected

text: house mouse

text: adult

text: wild type genotype

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: substantia nigra

text: Mus musculus

text: male

characteristic: strain

text: Sample 13

characteristic: title


E-MTAB-13244:Sample 14

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Petersburg Nuclear Physics Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13244:Sample 14

characteristic: Submitter Id

text: 8 to 12

characteristic: age

text: ArrayExpress

text: not collected

text: house mouse

text: adult

text: wild type genotype

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: substantia nigra

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: Sample 14


E-MTAB-13244:Sample 15

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Petersburg Nuclear Physics Institute

text: public

text: E-MTAB-13244:Sample 15

text: 8 to 12

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

text: Mus musculus

text: substantia nigra

text: Mus musculus

text: male

text: Sample 15


E-MTAB-13244:Sample 16

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Petersburg Nuclear Physics Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13244:Sample 16

text: 8 to 12

text: ArrayExpress

text: not collected

text: house mouse

text: adult

text: wild type genotype

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: substantia nigra

text: Mus musculus

text: male

characteristic: strain

text: Sample 16

characteristic: title


E-MTAB-13244:Sample 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Petersburg Nuclear Physics Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13244:Sample 2

characteristic: Submitter Id

text: 8 to 12

characteristic: age

text: ArrayExpress

text: not collected

text: house mouse

text: adult

text: wild type genotype

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: substantia nigra

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: Sample 2


E-MTAB-13244:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Petersburg Nuclear Physics Institute

text: public

text: E-MTAB-13244:Sample 3

text: 8 to 12

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

text: Mus musculus

text: substantia nigra

text: Mus musculus

text: male

text: Sample 3


E-MTAB-13244:Sample 4

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Petersburg Nuclear Physics Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13244:Sample 4

text: 8 to 12

text: ArrayExpress

text: not collected

text: house mouse

text: adult

text: wild type genotype

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: substantia nigra

text: Mus musculus

text: male

characteristic: strain

text: Sample 4

characteristic: title


E-MTAB-13244:Sample 5

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Petersburg Nuclear Physics Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13244:Sample 5

characteristic: Submitter Id

text: 8 to 12

characteristic: age

text: ArrayExpress

text: not collected

text: house mouse

text: adult

text: wild type genotype

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: substantia nigra

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: Sample 5


E-MTAB-13244:Sample 6

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Petersburg Nuclear Physics Institute

text: public

text: E-MTAB-13244:Sample 6

text: 8 to 12

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

text: Mus musculus

text: substantia nigra

text: Mus musculus

text: male

text: Sample 6


E-MTAB-13244:Sample 7

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Petersburg Nuclear Physics Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13244:Sample 7

text: 8 to 12

text: ArrayExpress

text: not collected

text: house mouse

text: adult

text: wild type genotype

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: substantia nigra

text: Mus musculus

text: male

characteristic: strain

text: Sample 7

characteristic: title


E-MTAB-13244:Sample 8

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Petersburg Nuclear Physics Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13244:Sample 8

characteristic: Submitter Id

text: 8 to 12

characteristic: age

text: ArrayExpress

text: not collected

text: house mouse

text: adult

text: wild type genotype

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: substantia nigra

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

text: Sample 8


E-MTAB-13244:Sample 9

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Petersburg Nuclear Physics Institute

text: public

text: E-MTAB-13244:Sample 9

text: 8 to 12

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

text: Mus musculus

text: substantia nigra

text: Mus musculus

text: male

text: Sample 9


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Shanghai Tenth People's Hospital

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Shanghai Tenth People's Hospital

text: ArrayExpress

text: not collected

text: Protocols: Strains were maintained at -80˚C. Strains were streaked on YPD plates. The plates were incubated at 37˚C overnight. Then several colonies were picked up and suspended in DDW. Cell density was adjusted to 10,000 cells/ml, then 100µl of cell suspension was plated on YPD plates. The plates were incubated at 37˚C overnight. Colonies were picked up and suspended in DDW, then cell pellets were obtained by centrifuging at highest speed for 1min. We used the phenol-chloroform method to extract Genomic DNA. Cell pellets were suspended in 200µl of lysis buffer, add 100µl of acid washed glass beads, and 0,2ml phenol:chloroform:isoamyl alcohol (25:24:1). Vortex for 30min at 4˚C. Add 200µl TE pH7.5. Centrifuge for 5min at maximum speed. Transfer aqueous layer to a new 1.5ml EP tube. Add 1ml 100% ethanol. Precipitate 1h at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard the supernatant. Add 400µl TE pH 7.5. Add 3ul of RNase A (10mg/ml). Incubate at 37˚C for 30min. Add 10µl of 3M NaOAc and 1ml of 100% ethanol. Mix by inversion. Precipitate 30min at -20˚C. Pellet DNA by centrifuging for 10min at maximum speed. Discard supernatant. Air-dry the pellet overnight. Resuspend in 50µl water. 1µg Genomic DNA was randomly fragmented by Covaris, followed by fragments selection by Agencourt AMPure XP-Medium kit to an average size of 200~400 bp. Selected fragments were end repaired and 3\"adenylate, then the adaptors were ligated to the end of these 3\"adenylate fragments. The products were amplified by PCR and purified by the Agencourt AMPure XP-Medium kit. The purified double stranded PCR products were heat denatured to single strand, then circularised by the splint oligo sequence. The single strand circle DNA (ssCirDNA) were formatted as the final library and qualified by QC.

text: not collected

text: not applicable

characteristic: isolate

text: Candida albicans

characteristic: organism

text: Candida albicans

text: whole organism

text: aneuploid

characteristic: ploidy

text: Candida albicans

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Director of Advanced Centre for Treatment, Research and Education in Cancer,  Professor of Medical Oncology, Tata Memorial Centre/Hospital & Homi Bhabha National Institute

characteristic: Submitter Id

text: ArrayExpress

text: Blood in P2

characteristic: clinical information

text: not collected

text: human

text: Protocols: Patients with histologically diagnosed breast cancer, progressed under any treatment modality, with a receptor phenotype that was negative for ER, PR, and HER2, and whose sites of progression were amenable to biopsy and who were previously operated upon at Tata Memorial Hospital, were eligible to be consented to participate in this study. We recruited nine patients to this study of whom 3 patients (P2, P4 and P7) could be followed longitudinally during the course of their therapy, while other 6 were lost to follow up after initial tissue bio banking at 1st progression. Patients P2, P4 and P7 were recruited at the time of their first progression post adjuvant chemo and radiotherapy. We bio-banked the tumour tissue from the first progression site in RNA-Later along with 15 ml blood in EDTA tubes. DNA from fresh-frozen and buffy coat samples was extracted using the Qiagen DNA mini kit (Cat No./ID: 51306). A total of 6 mL of plasma from each patient sample (except for one sample for which 3.6 mL blood was used) was used to extract ctDNA using the Circulating Nucleic Acid kit (Cat No./ID: 55114) from Qiagen® (Venlo, The Netherlands), according to the manufacturer’s instructions. Then, 6 mL ctDNA from each sample was eluted into 55 µL of AVE buffer and stored at −20°C. The concentration of the extracted ctDNA was determined using the Qubit dsDNA HS (High Sensitivity) Assay Kit (Invitrogen, Carlsbad, CA, USA), and the size distribution of ctDNA was assessed using Fragment analyzer. Deep sequencing was performed on selected somatic mutations that were identified using exome sequencing data (E-MTAB-11379). An AmpliSeq custom DNA panel (http://sapac.support.illumina.com/downloads/ampliseq-for-illumina-custom-and-community-panels-reference-guide-1000000036408.html) was designed for library preparation. Targets were amplified using PCR (16 cycles at 99°C for 15 sec and 60°C for 4 min). The amplicons (125 bp/mutation) generated from this step were subjected to partial digestion (using the FuPa reagent), followed by indexing and cleaning using AMPureXP beads. This was followed by one more round of PCR amplification (7 cycles at 98°C for 15 sec and 64°C for 1 min) and subsequent cleaning using AMPure XP beads.

text: adult

text: triple negative breast cancer

characteristic: disease

text: Blood

characteristic: disease staging

text: blood DNA

characteristic: fraction

text: not collected

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

text: Deep sequencing using AmpliSeq custom DNA panel with HiSeq2000 at ~30,000x.

characteristic: protocol

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Director of Advanced Centre for Treatment, Research and Education in Cancer,  Professor of Medical Oncology, Tata Memorial Centre/Hospital & Homi Bhabha National Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: 1st Progression in P2

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: triple negative breast cancer

text: Progression/Relapse

text: tumour DNA

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: 1st Progression ctDNA in P2

characteristic: clinical information

text: not collected

text: human

text: adult

text: triple negative breast cancer

characteristic: disease

text: Progression/Relapse

characteristic: disease staging

text: ctDNA

characteristic: fraction

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: 2nd Progression in P2

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: adult

text: triple negative breast cancer

text: Progression/Relapse

text: tumour DNA

text: not collected

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: protocol

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: 2nd Progression ctDNA in P2

text: not collected

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: triple negative breast cancer

text: Progression/Relapse

text: ctDNA

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: 3rd Progression in P2

characteristic: clinical information

text: not collected

characteristic: collection date

text: human

text: adult

text: triple negative breast cancer

characteristic: disease

text: Progression/Relapse

characteristic: disease staging

text: tumour DNA

characteristic: fraction

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: 3rd Progression ctDNA in P2

text: not collected

text: human

characteristic: common name

text: adult

text: triple negative breast cancer

text: Progression/Relapse

text: ctDNA

text: not collected

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: protocol

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: Surgery in P2

characteristic: clinical information

text: not collected

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: triple negative breast cancer

text: Surgical Specimen

text: tumour DNA

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Blood in P4

text: not collected

characteristic: collection date

text: human

text: adult

text: triple negative breast cancer

characteristic: disease

text: Blood

characteristic: disease staging

text: blood DNA

characteristic: fraction

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: 1st Progression in P4

characteristic: clinical information

text: not collected

text: human

characteristic: common name

text: adult

text: triple negative breast cancer

text: Progression/Relapse

text: tumour DNA

text: not collected

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: protocol

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: 1st Progression ctDNA in P4

text: not collected

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: triple negative breast cancer

text: Progression/Relapse

text: ctDNA

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: 2nd Progression in P4

characteristic: clinical information

text: not collected

characteristic: collection date

text: human

text: adult

text: triple negative breast cancer

characteristic: disease

text: Progression/Relapse

characteristic: disease staging

text: tumour DNA

characteristic: fraction

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: 2nd Progression ctDNA in P4

text: not collected

text: human

characteristic: common name

text: adult

text: triple negative breast cancer

text: Progression/Relapse

text: ctDNA

text: not collected

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: protocol

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: Diagnostic Biopsy in P7

characteristic: clinical information

text: not collected

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: triple negative breast cancer

text: Primary Tumour

text: tumour DNA

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: Blood in P7

text: not collected

characteristic: collection date

text: human

text: adult

text: triple negative breast cancer

characteristic: disease

text: Blood

characteristic: disease staging

text: blood DNA

characteristic: fraction

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: 1st Progression in P7

characteristic: clinical information

text: not collected

text: human

characteristic: common name

text: adult

text: triple negative breast cancer

text: Progression/Relapse

text: tumour DNA

text: not collected

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: protocol

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: 1st Progression ctDNA in P7

text: not collected

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: triple negative breast cancer

text: Progression/Relapse

text: ctDNA

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: 2nd Progression in P7

characteristic: clinical information

text: not collected

characteristic: collection date

text: human

text: adult

text: triple negative breast cancer

characteristic: disease

text: Progression/Relapse

characteristic: disease staging

text: tumour DNA

characteristic: fraction

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: 2nd Progression ctDNA in P7

text: not collected

text: human

characteristic: common name

text: adult

text: triple negative breast cancer

text: Progression/Relapse

text: ctDNA

text: not collected

characteristic: individual

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

characteristic: organism part

characteristic: protocol

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: 3rd Progression in P7

characteristic: clinical information

text: not collected

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: triple negative breast cancer

text: Progression/Relapse

text: tumour DNA

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: breast

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: 3rd Progression ctDNA in P7

text: not collected

characteristic: collection date

text: human

text: adult

text: triple negative breast cancer

characteristic: disease

text: Progression/Relapse

characteristic: disease staging

text: ctDNA

characteristic: fraction

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: breast

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Goethe University Frankfurt

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Goethe University Frankfurt

text: Lisa M. Schulte

text: Ptychohyla macrotympanum male ventrolateral gland

text: Mexico

text: Chiapas

characteristic: geographic location (region and locality)

text: Ptychohyla macrotympanum

text: Ptychohyla macrotympanum

text: male

characteristic: sex

text: ventrolateral gland

text: Ptychohyla macrotympanum ventrolateral gland RNAseq


characteristic: ENA-CHECKLIST

text: Goethe University Frankfurt

text: public

text: Lisa M. Schulte

text: Ptychohyla macrotympanum male nuptial pad

characteristic: description

text: Mexico

characteristic: geographic location (country and/or sea)

text: Chiapas

text: Ptychohyla macrotympanum

characteristic: organism

text: Ptychohyla macrotympanum

text: male

text: nuptial pad (thumb)

text: Ptychohyla macrotympanum nuptial pad RNAseq


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Istituto di Ricerche Farmacologiche \"Mario Negri\" IRCCS

text: ArrayExpress

characteristic: broker name

text: induced pluripotent stem cell

text: not collected

text: human

characteristic: common name

text: Protocols: Collection of 50000 cells per replicate and resuspension of the pellet in TRIzol buffer - Resuspension of nuclei in the transposition reaction mix- Incubation of the transposition reaction- Purification using Qiagen MinElute PCR Purification Kit- Elution of transposed DNA in Elution BufferRefer to DOI: 10.1002/0471142727.mb2129s109 - Amplification of DNA fragments- Purification of amplified library using Qiagen MinElute PCR Purification Kit

text: Cornelia de Lange syndrome

text: corrected heterozygous missense point-mutation of the NIPBL gene

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Istituto di Ricerche Farmacologiche \"Mario Negri\" IRCCS

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: induced pluripotent stem cell

text: not collected

characteristic: collection date

text: human

text: Cornelia de Lange syndrome

characteristic: disease

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

text: public

text: ArrayExpress

text: induced pluripotent stem cell

text: not collected

text: human

characteristic: description

text: Cornelia de Lange syndrome

text: heterozygous missense point-mutation of the NIPBL gene

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: induced pluripotent stem cell

text: not collected

text: human

characteristic: common name

text: normal

text: wild type genotype

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: induced pluripotent stem cell

text: not collected

text: human

text: normal

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

text: Post Doctoral Fellow

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: house mouse

text: Protocols: Freshly harvested tumors from Trem1+/+and Trem1-/- mice were pooled separately into 2 groups to maximize the isolation of tumor infiltrating myeloid cells. Tumors were gently dissociated using the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotech). Single-cell suspensions of tumor cells were purified by incubation with CD11b Microbeads (Miltenyi Biotec, cat. no. 130-049-601) as per the manufacturer’s instructions to enrich the tumor-infiltrating myeloid cells. Quality and quantity of cells were assessed under the microscope by trypan blue staining, and dead cells were removed using theDead Cell Removal Kit (STEMCELL, cat. no. 17899) as per the manufacturer’s instructions. Nuclei acid extraction was performed following the manufacturer's instructions (10x Genomics, as part of the Chromium Single Cell 3' v3.1). We assayed up to 4200 isolated CD45+CD11b+ cells from the TME of the B16F10 melanoma model with a coverage rate of 18,854 genes per cell. scRNA-seq libraries were generated using ChromiumNext GEM Single Cell 3’ Reagent kit v3.1 (10x Genomics) according to the manufacturer’s protocol.

text: control

characteristic: genetic modification

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: tumor

characteristic: sampling site

text: Mus musculus

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: Post Doctoral Fellow

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: not collected

text: house mouse

characteristic: description

text: gene knock out

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: tumor

text: Mus musculus


name: E-MTAB-13248:SHAPE-Seq U2 snRNA in vitro DMSO

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

tag: Namespace:Institute of Molecular Genetics of the Czech Academy of Science

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: Protocols: For the in vitro experiment, U2WT and U4 pre-snRNA were transcribed by T7 polymerase P266L variant 98 from pcDNA3 or p-MA-T plasmids, respectively with T7 promoter followed by DNase I (30 min at 37 °C) and Proteinase K (30 min at 37°C) treatments.For the ex vivo experiment, RNA was isolated from HeLa cells. Cells were washed 3x with 1xPBS, dissociated by Trypsin-EDTA solution (Sigma) and collected by centrifugation at 500 g and 4°C for 5 min. Cells were resuspended in 5 ml lysis buffer (40 mM Tris-HCl pH 8.0, 25 mM NaCl, 6 mM MgCl2, 1 mM CaCl2, 256 mM sucrose, 1000 U/ml SUPERase-IN RNAse inhibitor, 0.5% Triton X-100, 450 U/ml DNAse I), rotated 5 min at 4°C and pelleted at 2250 g for 2 min at 4°C. The pellet was resuspended in proteinase K buffer (100 mM Tris-HCl pH 7.5, 200 mM NaCl, 2 mM EDTA, 1% SDS, 500 µg/ml Protease K) and incubated at room temperature for 45 min.For the in vivo experiment, we started with 10x106 HeLa cells. Cells were 1x washed by 1xPBS and collected by centrifugation for 5 min at 10,000 g and 4°C. The pellet was resuspended in 500 µl 1x PBS and split into two tubes. For in vitro experiment, RNA was folded for 30 min at 37°C in 57 mM MgCl2 for U2 snRNA and 60 mM MgCl2 for U4 pre-snRNA, followed by labeling with 100 mM NAI at 37°C for 10 min. DMSO was used as a negative control. For ex vivo experiment, 100mM NAI or DMSO was added to RNA and incubated for 10 min at 37°C. For in vivo experiment, NAI or DMSO to final concentration 200 mM was added and cells were incubated for 10 min at 37°C. For the in vitro experiment, U2 snRNA was purified on 30 kDa Amicon columns; U4 pre-snRNA was purified on Superdex 200 Increase 10/300GL colomn pre-equilibrated with filtration buffer (50 mM K-HEPES pH 7.4, 150 mM KCl, 0.1 mM EDTA). For ex vivo experiment, pre-equilibrated phenol/chloroform/isoamyl alcohol buffered by folding buffer (110 mM HEPES pH 8.0, 110 mM KCl, 11 mM MgCl2) was added after the Proteinase K treatment, and samples were centrifuged at 12,000 g for 15 min at 4°C. RNA was cleaned on a PD-10 column according to the manufacturer’s instructions. For in vivo experiment, RNA was isolated using Trizol (Sigma) and 200 µl chloroform and precipitated with ethanol at -20°C overnight. All prepared RNA samples (in vitro, ex vivo, in vivo) were used for reverse transcription with the gene-specific primer 5’-CGTTCCTGGAGGTACTGCAA for U2 snRNA and 5’- AAAAATTCAGTCTCCG for U4 pre-snRNA. We used SHAPE MaP buffer (50 mM Tris-HCl pH 8.0, 75 mM KCl, 10 mM DTT, 0.5 mM dNTP, 6 mM MnCl2) and SuperScript II (Invitrogen). Amplicons for snRNAs were generated using gene-specific forward and reverse primers. Importantly, the primers include Nextera adaptors required for downstream library construction. All gene-specific and adaptor sequences used are detailed in Table S2. Gene-specific amplicons were generated using these primers, 5µL of purified cDNA, and NEBNext Ultra II Q5 MasterMix (Cat. No. M0544L). PCR reaction products were cleaned using Monarch PCR&DNA Clean-up Kits (NEB, Cat. No. T1030S) and a binding buffer:sample ratio of 5:1. Remaining Illumina adaptor sequences were added using the PCR MasterMix and index primers provided in the NexteraXT DNA Library Preparation Kit (Illumina) according to the manufacturer’s protocol, but using 1/5th the suggested reaction volumes. Libraries were quantified using Qubit (Invitrogen) and BioAnalyzer (Agilent).

text: not collected

text: in vitro 57 mM MgCl2

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: U2 snRNA

characteristic: sample

text: Homo sapiens

text: SHAPE-Seq U2 snRNA in vitro DMSO

text: DMSO

characteristic: treatment


name: E-MTAB-13248:SHAPE-Seq U2 snRNA in vitro NAI

characteristic: ENA-CHECKLIST

text: Institute of Molecular Genetics of the Czech Academy of Science

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

text: not collected

text: in vitro 57 mM MgCl2

text: Homo sapiens

text: Homo sapiens

text: U2 snRNA

text: Homo sapiens

text: SHAPE-Seq U2 snRNA in vitro NAI

text: 100 mM NAI


name: E-MTAB-13248:SHAPE-Seq U4 pre-snRNA in vitro DMSO

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: not collected

text: human

text: not collected

text: in vitro 60 mM MgCl2

text: Homo sapiens

text: Homo sapiens

text: U4 pre-snRNA

text: Homo sapiens

text: SHAPE-Seq U4 pre-snRNA in vitro DMSO

characteristic: title

text: DMSO


name: E-MTAB-13248:SHAPE-Seq U4 pre-snRNA in vitro NAI

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: not collected

text: human

characteristic: description

text: not collected

characteristic: geographic location (country and/or sea)

text: in vitro 60 mM MgCl2

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: U4 pre-snRNA

text: Homo sapiens

text: SHAPE-Seq U4 pre-snRNA in vitro NAI

text: 100 mM NAI


name: E-MTAB-13248:SHAPE-Seq U2 snRNA ex vivo DMSO

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

text: not collected

text: ex vivo HeLa cells

text: Homo sapiens

text: Homo sapiens

text: U2 snRNA

text: Homo sapiens

text: SHAPE-Seq U2 snRNA ex vivo DMSO

text: DMSO


name: E-MTAB-13248:SHAPE-Seq U2 snRNA ex vivo NAI

text: public

text: ArrayExpress

text: not collected

text: human

characteristic: common name

text: not collected

text: ex vivo HeLa cells

characteristic: growth condition

text: Homo sapiens

text: Homo sapiens

text: U2 snRNA

characteristic: sample

text: Homo sapiens

text: SHAPE-Seq U2 snRNA ex vivo NAI

text: 100 mM NAI

characteristic: treatment


name: E-MTAB-13248:SHAPE-Seq U2 snRNA in vivo DMSO

characteristic: ENA-CHECKLIST

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

text: not collected

text: in vivo HeLa cells

text: Homo sapiens

text: Homo sapiens

text: U2 snRNA

text: Homo sapiens

text: SHAPE-Seq U2 snRNA in vivo DMSO

text: 200 mM DMSO


name: E-MTAB-13248:SHAPE-Seq U2 snRNA in vivo NAI

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: not collected

text: human

text: not collected

text: in vivo HeLa cells

text: Homo sapiens

text: Homo sapiens

text: U2 snRNA

text: Homo sapiens

text: SHAPE-Seq U2 snRNA in vivo NAI

characteristic: title

text: 200 mM NAI


characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch

text: ArrayExpress

text: HaCaT

text: keratinocyte

text: not collected

text: human

text: Protocols: Cells growing on the culture dishes were washed twice with ice-cold calcium/magnesium free PBS and next were submerged with RNA extraction buffer and scraped off using rubber tipped cell scraper. The suspension was immediately snap-frozen in dry ice and stored at -70°C until the total RNA extraction procedure. CRISPR/Cas9-modified HaCaT cells were plated onto dishes at high seeding density (500 000/dish) and maintained without sub-culturing for 3 days in submerged culture in a standard DMEM high glucose medium supplemented with 10% FBS. Wild type HaCaT cells were modified by CRISPR-Cas9 gene editing system to generate HSPA2-null isogenic clones. In brief, cells were transfected with HSPA2 Double Nickase Plasmid (Santa Cruz Biotechnology) and Lipofectamine 3000. Transfected cells were selected in a standard culture medium (high glucose DMEM/FBS) containing puromycin (1 µg/mL). Afterwards, single clones were obtained by limiting dilution on 96-well plates. Disruption of the HSPA2 gene in clones was examined at protein level by Western blot and confirmed by Sanger sequencing. Six individual isogenic clones with the non-edited HSPA2 gene sequence were pooled as control CRISPR-CTR clones; four isogenic gene-edited clones with mutated HSPA2 sequence and a full protein loss were pooled and named CRISPR-4, pool containing two different HSPA2-null clones was named CRISPR-2B. Total RNA was extracted using the GeneJET RNA Purification Kit in accordance with the manufacturer’s protocol. RNA samples were purified from contaminating DNA by treatment with RNase-free DNase I, possible DNA contamination was examined also by a control PCR reaction. 100 ng RNA was used for library preparation Sequencing library was prepared according to the standard Illumina protocol using the TruSeq Stranded mRNA library preparation kit.

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: CRISPR/Cas 9 HSPA2 no gRNA

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

characteristic: organism part

text: biological replicate 1

characteristic: replicate

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Maria Sklodowska-Curie National Research Institute of Oncology Gliwice Branch

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: HaCaT

text: keratinocyte

text: not collected

text: human

characteristic: common name

text: adult

text: normal

text: CRISPR/Cas9 HSPA2 knockout gRNA 4

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: biological replicate 1

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: HaCaT

text: keratinocyte

text: not collected

characteristic: collection date

text: human

text: adult

text: normal

text: CRISPR/Cas9 HSPA2 knockout gRNA 2B

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: biological replicate 1

text: Homo sapiens

characteristic: title


text: public

text: ArrayExpress

text: HaCaT

text: keratinocyte

text: not collected

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: CRISPR/Cas 9 HSPA2 no gRNA

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: biological replicate 2

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: ArrayExpress

text: HaCaT

text: keratinocyte

text: not collected

text: human

text: adult

text: normal

text: CRISPR/Cas9 HSPA2 knockout gRNA 4

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

text: biological replicate 2

characteristic: replicate

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: HaCaT

text: keratinocyte

text: not collected

text: human

characteristic: common name

text: adult

text: normal

text: CRISPR/Cas9 HSPA2 knockout gRNA 2B

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: biological replicate 2

text: Homo sapiens


text: public

text: ArrayExpress

text: HaCaT

text: keratinocyte

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: CRISPR/Cas 9 HSPA2 no gRNA

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: biological replicate 3

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: ArrayExpress

text: HaCaT

text: keratinocyte

text: not collected

text: human

text: adult

text: normal

text: CRISPR/Cas9 HSPA2 knockout gRNA 4

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: biological replicate 3

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: HaCaT

text: keratinocyte

text: not collected

text: human

text: adult

text: normal

text: CRISPR/Cas9 HSPA2 knockout gRNA 2B

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

text: biological replicate 3

characteristic: replicate

text: Homo sapiens


E-MTAB-13250:Sample 10

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13250:Sample 10

tag: Namespace:Quadram Institute Biosciences

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

text: Protocols: The E. coli transposon mutant library used in this study was described by Yasir et al. (2020), and the S. Typhimurium library was described by Holden et al. (2022). The transposon-located promoter was induced with 1 mM IPTG in both E. coli and S. Typhimurium. For each condition, approximately 107 CFU/mL of the transposon mutant library was added to 10 mL LB broth supplemented with the corresponding concentration of antimicrobial. Each of the three analogues (003, 009 and 010) of OPT-2U1 were investigated at four concentrations around the MIC: ¼xMIC, ½xMIX, 1xMIC and 2xMIC, as well as an unstressed control. This corresponded to 8, 16, 32 and 64 µg/mL respectively. Conditions were then incubated for 24 hours at 37 ⁰C lightly shaken at 200 rpm. Following this, 1 mL of each culture was centrifuged to form a bacterial pellet. DNA was extracted from these pellets following the protocol outlined by Trampari et al. (2021). Genomic DNA was normalised to 11.1 ng/µL and tagmented using a MuSeek DNA fragment library preparation kit (ThermoFisher). Fragmented DNA was purified with AMPure XP beads (Beckman Coulter). DNA was amplified using primers customised for the tagmented ends of the DNA and biotinylated primers specific to transposon. Following another purification step, biotinylated fragmented DNA was incubated for 4 hours with streptavidin beads (Dynabeads® kilobaseBINDER™, Invitrogen) to capture only DNA fragments containing the transposon. A second PCR step using DNA bound to the beads used barcoded sequencing primers specific to the tagmented ends and to the transposon. Beads were removed from the reaction with a magnet and DNA was purified and size-selected using AMPure beads. Fragment length was quantified using a Tapestation (Aligent).

characteristic: description

text: transposon mutant library

characteristic: genotype

text: not collected

text: LB Broth

characteristic: growth condition

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 10


E-MTAB-13250:Sample 29

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13250:Sample 29

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

characteristic: geographic location (country and/or sea)

text: LB Broth

text: not applicable

text: Salmonella enterica subsp. enterica serovar Typhimurium

text: whole organism

text: Sample 29

characteristic: title


E-MTAB-13250:Sample 3

characteristic: ENA-FIRST-PUBLIC

text: Quadram Institute Biosciences

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: E-MTAB-13250:Sample 3

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

characteristic: isolate

text: Escherichia coli K-12

characteristic: organism

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 3


E-MTAB-13250:Sample 30

characteristic: ENA-LAST-UPDATE

text: Quadram Institute Biosciences

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13250:Sample 30

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

text: whole organism

characteristic: organism part

text: Sample 30


E-MTAB-13250:Sample 31

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13250:Sample 31

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

characteristic: description

text: transposon mutant library

characteristic: genotype

text: not collected

text: LB Broth

text: not applicable

text: whole organism

text: Sample 31


E-MTAB-13250:Sample 32

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13250:Sample 32

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

characteristic: growth condition

text: not applicable

text: whole organism

text: Sample 32


E-MTAB-13250:Sample 33

characteristic: ENA-FIRST-PUBLIC

text: Quadram Institute Biosciences

characteristic: INSDC first public

text: public

text: E-MTAB-13250:Sample 33

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

characteristic: geographic location (country and/or sea)

text: LB Broth

text: not applicable

text: whole organism

text: Sample 33

characteristic: title


E-MTAB-13250:Sample 34

characteristic: ENA-LAST-UPDATE

text: Quadram Institute Biosciences

text: public

characteristic: SRA accession

text: E-MTAB-13250:Sample 34

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

characteristic: isolate

characteristic: organism

text: whole organism

text: Sample 34


E-MTAB-13250:Sample 35

text: Quadram Institute Biosciences

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13250:Sample 35

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

text: whole organism

characteristic: organism part

text: Sample 35


E-MTAB-13250:Sample 36

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13250:Sample 36

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

characteristic: description

text: transposon mutant library

characteristic: genotype

text: not collected

text: LB Broth

text: not applicable

text: whole organism

text: Sample 36


E-MTAB-13250:Sample 4

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13250:Sample 4

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

characteristic: growth condition

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 4


E-MTAB-13250:Sample 5

characteristic: ENA-FIRST-PUBLIC

text: Quadram Institute Biosciences

characteristic: INSDC first public

text: public

text: E-MTAB-13250:Sample 5

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

characteristic: geographic location (country and/or sea)

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 5

characteristic: title


E-MTAB-13250:Sample 6

characteristic: ENA-LAST-UPDATE

text: Quadram Institute Biosciences

text: public

characteristic: SRA accession

text: E-MTAB-13250:Sample 6

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

characteristic: isolate

text: Escherichia coli K-12

characteristic: organism

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 6


E-MTAB-13250:Sample 7

text: Quadram Institute Biosciences

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13250:Sample 7

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

characteristic: organism part

text: Escherichia coli K-12

text: Sample 7


E-MTAB-13250:Sample 8

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13250:Sample 8

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

characteristic: description

text: transposon mutant library

characteristic: genotype

text: not collected

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 8


E-MTAB-13250:Sample 9

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13250:Sample 9

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

characteristic: growth condition

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 9


E-MTAB-13250:Sample 11

characteristic: ENA-FIRST-PUBLIC

text: Quadram Institute Biosciences

characteristic: INSDC first public

text: public

text: E-MTAB-13250:Sample 11

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

characteristic: geographic location (country and/or sea)

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 11

characteristic: title


E-MTAB-13250:Sample 12

characteristic: ENA-LAST-UPDATE

text: Quadram Institute Biosciences

text: public

characteristic: SRA accession

text: E-MTAB-13250:Sample 12

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

characteristic: isolate

text: Escherichia coli K-12

characteristic: organism

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 12


E-MTAB-13250:Sample 13

text: Quadram Institute Biosciences

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13250:Sample 13

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

characteristic: organism part

text: Escherichia coli K-12

text: Sample 13


E-MTAB-13250:Sample 14

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13250:Sample 14

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

characteristic: description

text: transposon mutant library

characteristic: genotype

text: not collected

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 14


E-MTAB-13250:Sample 15

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13250:Sample 15

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

characteristic: growth condition

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 15


E-MTAB-13250:Sample 16

characteristic: ENA-FIRST-PUBLIC

text: Quadram Institute Biosciences

characteristic: INSDC first public

text: public

text: E-MTAB-13250:Sample 16

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

characteristic: geographic location (country and/or sea)

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 16

characteristic: title


E-MTAB-13250:Sample 17

characteristic: ENA-LAST-UPDATE

text: Quadram Institute Biosciences

text: public

characteristic: SRA accession

text: E-MTAB-13250:Sample 17

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

characteristic: isolate

text: Escherichia coli K-12

characteristic: organism

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 17


E-MTAB-13250:Sample 18

text: Quadram Institute Biosciences

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13250:Sample 18

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

characteristic: organism part

text: Escherichia coli K-12

text: Sample 18


E-MTAB-13250:Sample 37

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13250:Sample 37

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

characteristic: description

text: transposon mutant library

characteristic: genotype

text: not collected

text: LB Broth

text: not applicable

text: whole organism

text: Sample 37


E-MTAB-13250:Sample 38

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13250:Sample 38

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

characteristic: growth condition

text: not applicable

text: whole organism

text: Sample 38


E-MTAB-13250:Sample 39

characteristic: ENA-FIRST-PUBLIC

text: Quadram Institute Biosciences

characteristic: INSDC first public

text: public

text: E-MTAB-13250:Sample 39

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

characteristic: geographic location (country and/or sea)

text: LB Broth

text: not applicable

text: whole organism

text: Sample 39

characteristic: title


E-MTAB-13250:Sample 40

characteristic: ENA-LAST-UPDATE

text: Quadram Institute Biosciences

text: public

characteristic: SRA accession

text: E-MTAB-13250:Sample 40

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

characteristic: isolate

characteristic: organism

text: whole organism

text: Sample 40


E-MTAB-13250:Sample 41

text: Quadram Institute Biosciences

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13250:Sample 41

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

text: whole organism

characteristic: organism part

text: Sample 41


E-MTAB-13250:Sample 42

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13250:Sample 42

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

characteristic: description

text: transposon mutant library

characteristic: genotype

text: not collected

text: LB Broth

text: not applicable

text: whole organism

text: Sample 42


E-MTAB-13250:Sample 43

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13250:Sample 43

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

characteristic: growth condition

text: not applicable

text: whole organism

text: Sample 43


E-MTAB-13250:Sample 44

characteristic: ENA-FIRST-PUBLIC

text: Quadram Institute Biosciences

characteristic: INSDC first public

text: public

text: E-MTAB-13250:Sample 44

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

characteristic: geographic location (country and/or sea)

text: LB Broth

text: not applicable

text: whole organism

text: Sample 44

characteristic: title


E-MTAB-13250:Sample 19

characteristic: ENA-LAST-UPDATE

text: Quadram Institute Biosciences

text: public

characteristic: SRA accession

text: E-MTAB-13250:Sample 19

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

characteristic: isolate

text: Escherichia coli K-12

characteristic: organism

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 19


E-MTAB-13250:Sample 20

text: Quadram Institute Biosciences

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13250:Sample 20

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

characteristic: organism part

text: Escherichia coli K-12

text: Sample 20


E-MTAB-13250:Sample 21

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13250:Sample 21

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

characteristic: description

text: transposon mutant library

characteristic: genotype

text: not collected

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 21


E-MTAB-13250:Sample 22

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13250:Sample 22

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

characteristic: growth condition

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 22


E-MTAB-13250:Sample 23

characteristic: ENA-FIRST-PUBLIC

text: Quadram Institute Biosciences

characteristic: INSDC first public

text: public

text: E-MTAB-13250:Sample 23

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

characteristic: geographic location (country and/or sea)

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 23

characteristic: title


E-MTAB-13250:Sample 24

characteristic: ENA-LAST-UPDATE

text: Quadram Institute Biosciences

text: public

characteristic: SRA accession

text: E-MTAB-13250:Sample 24

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

characteristic: isolate

text: Escherichia coli K-12

characteristic: organism

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 24


E-MTAB-13250:Sample 25

text: Quadram Institute Biosciences

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13250:Sample 25

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

characteristic: organism part

text: Escherichia coli K-12

text: Sample 25


E-MTAB-13250:Sample 26

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13250:Sample 26

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

characteristic: description

text: transposon mutant library

characteristic: genotype

text: not collected

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 26


E-MTAB-13250:Sample 45

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13250:Sample 45

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

characteristic: growth condition

text: not applicable

text: whole organism

text: Sample 45


E-MTAB-13250:Sample 46

characteristic: ENA-FIRST-PUBLIC

text: Quadram Institute Biosciences

characteristic: INSDC first public

text: public

text: E-MTAB-13250:Sample 46

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

characteristic: geographic location (country and/or sea)

text: LB Broth

text: not applicable

text: whole organism

text: Sample 46

characteristic: title


E-MTAB-13250:Sample 47

characteristic: ENA-LAST-UPDATE

text: Quadram Institute Biosciences

text: public

characteristic: SRA accession

text: E-MTAB-13250:Sample 47

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

characteristic: isolate

characteristic: organism

text: whole organism

text: Sample 47


E-MTAB-13250:Sample 48

text: Quadram Institute Biosciences

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13250:Sample 48

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

text: whole organism

characteristic: organism part

text: Sample 48


E-MTAB-13250:Sample 49

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13250:Sample 49

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

characteristic: description

text: transposon mutant library

characteristic: genotype

text: not collected

text: LB Broth

text: not applicable

text: whole organism

text: Sample 49


E-MTAB-13250:Sample 50

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13250:Sample 50

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

characteristic: growth condition

text: not applicable

text: whole organism

text: Sample 50


E-MTAB-13250:Sample 51

characteristic: ENA-FIRST-PUBLIC

text: Quadram Institute Biosciences

characteristic: INSDC first public

text: public

text: E-MTAB-13250:Sample 51

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

characteristic: geographic location (country and/or sea)

text: LB Broth

text: not applicable

text: whole organism

text: Sample 51

characteristic: title


E-MTAB-13250:Sample 1

characteristic: ENA-LAST-UPDATE

text: Quadram Institute Biosciences

text: public

characteristic: SRA accession

text: E-MTAB-13250:Sample 1

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

characteristic: isolate

text: Escherichia coli K-12

characteristic: organism

text: Escherichia coli K-12

text: whole organism

text: Escherichia coli K-12

text: Sample 1


E-MTAB-13250:Sample 2

text: Quadram Institute Biosciences

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13250:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

text: not applicable

text: Escherichia coli K-12

text: Escherichia coli K-12

text: whole organism

characteristic: organism part

text: Escherichia coli K-12

text: Sample 2


E-MTAB-13250:Sample 27

text: Quadram Institute Biosciences

text: public

text: E-MTAB-13250:Sample 27

text: ArrayExpress

characteristic: broker name

text: not collected

characteristic: collection date

characteristic: description

text: transposon mutant library

characteristic: genotype

text: not collected

text: LB Broth

text: not applicable

text: whole organism

text: Sample 27


E-MTAB-13250:Sample 28

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Quadram Institute Biosciences

characteristic: INSDC center name

text: public

text: E-MTAB-13250:Sample 28

text: ArrayExpress

text: not collected

text: transposon mutant library

text: not collected

text: LB Broth

characteristic: growth condition

text: not applicable

text: whole organism

text: Sample 28


characteristic: ENA-FIRST-PUBLIC

text: KAUST

characteristic: INSDC first public

text: public

text: Tahala Reef

characteristic: Reef

text: Bacterium isolated from Styllophora pistillata Clade IV

text: Saudi Arabia

characteristic: geographic location (country and/or sea)

text: Halomonas sp. BMC6

text: Halomonas sp. BMC6

text: BMC6 isolate

characteristic: title


characteristic: ENA-LAST-UPDATE

text: KAUST

characteristic: INSDC last update

text: public

text: Aquarium Reef

characteristic: SRA accession

text: Bacterium isolated from Galaxea fascicularis

text: Saudi Arabia

text: Sutcliffiella sp. BMC8

characteristic: organism

text: Sutcliffiella sp. BMC8

text: BMC8 isolate


text: public

characteristic: INSDC status

tag: Namespace:MONASH INSTITUTE OF MEDICAL RESEARCH - MONASH UNIVERSITY

characteristic: Submitter Id

text: Bacterial isolate cultured from a mucosal sample

text: Australia

text: Bacteroides stercoris

text: Bacteroides stercoris


text: MONASH INSTITUTE OF MEDICAL RESEARCH - MONASH UNIVERSITY

text: public

characteristic: collection date

characteristic: description

text: Australia

text: Bacteroides stercoris

text: Bacteroides stercoris


characteristic: ENA-CHECKLIST

text: public

text: Australia

text: Escherichia coli IS25

text: Escherichia coli IS25


characteristic: External Id

text: public

text: Australia

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron


characteristic: INSDC center name

text: public

text: Bacterial isolate from mucosal sample

text: Australia

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron


text: public

text: Bacterial isolate from mucosal sample

text: Australia

text: [Ruminococcus] torques

text: [Ruminococcus] torques


text: public

text: Bacterial isolate from mucosal sample

text: Australia

text: Bacteroides stercoris

text: Bacteroides stercoris


text: public

text: Bacterial isolate cultured from a facael sample

text: Australia

text: Phocaeicola vulgatus

text: Phocaeicola vulgatus


text: public

text: Australia

text: Bacteroides caccae CL03T12C61

text: Bacteroides caccae CL03T12C61


text: public

text: Australia

text: Bifidobacterium longum

text: Bifidobacterium longum


text: public

text: Bacterial isolate from mucosal sample

text: Australia

text: Bifidobacterium longum

text: Bifidobacterium longum


text: public

text: Australia

text: Parafannyhessea umbonata

text: Parafannyhessea umbonata


text: public

text: Australia

text: Bifidobacterium adolescentis ATCC 15703

text: Bifidobacterium adolescentis ATCC 15703


text: public

text: Australia

text: Bacteroides eggerthii DSM 20697

text: Bacteroides eggerthii DSM 20697


text: public

text: Australia

text: Bacteroides ovatus CL02T12C04

text: Bacteroides ovatus CL02T12C04


text: public

text: Australia

text: Bacteroides caccae CL03T12C61

text: Bacteroides caccae CL03T12C61


text: public

text: Australia

text: Bacteroides faecis MAJ27

text: Bacteroides faecis MAJ27


text: public

text: Australia

text: Escherichia coli

text: Escherichia coli


text: public

text: Australia

text: Fusobacterium varium

text: Fusobacterium varium


text: public

text: Australia

text: Escherichia coli IS25

text: Escherichia coli IS25


text: public

text: Australia

text: Phocaeicola vulgatus ATCC 8482

text: Phocaeicola vulgatus ATCC 8482


text: public

text: Australia

text: Phocaeicola plebeius DSM 17135

text: Phocaeicola plebeius DSM 17135


text: public

text: Australia

text: Parabacteroides distasonis

text: Parabacteroides distasonis


text: public

text: Australia

text: Bacteroides fragilis

text: Bacteroides fragilis


text: public

text: Australia

text: Actinobacillus succinogenes

text: Actinobacillus succinogenes


text: public

text: Australia

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron


text: public

text: Australia

text: Clostridium perfringens

text: Clostridium perfringens


text: public

text: Australia

text: Enterococcus faecalis

text: Enterococcus faecalis


text: public

text: Australia

text: Enterococcus faecium UC8668

text: Enterococcus faecium UC8668


text: public

text: Australia

text: Clostridium perfringens SM101

text: Clostridium perfringens SM101


text: public

text: Australia

text: Bacteroides caccae CL03T12C61

text: Bacteroides caccae CL03T12C61


text: public

text: Australia

text: Bifidobacterium adolescentis

text: Bifidobacterium adolescentis


text: public

text: Australia

text: Catenibacterium mitsuokai

text: Catenibacterium mitsuokai


text: public

text: Australia

text: Thomasclavelia spiroformis

text: Thomasclavelia spiroformis


text: public

text: Australia

text: Bacteroides uniformis

text: Bacteroides uniformis


text: public

text: Australia

text: Bifidobacterium adolescentis ATCC 15703

text: Bifidobacterium adolescentis ATCC 15703


text: public

text: Australia

text: Clostridium perfringens CPE str. F4969

text: Clostridium perfringens CPE str. F4969


text: public

text: Australia

text: Collinsella aerofaciens ATCC 25986

text: Collinsella aerofaciens ATCC 25986


text: public

text: Australia

text: Bifidobacterium longum subsp. longum KACC 91563


text: public

text: Australia

text: Bifidobacterium longum

text: Bifidobacterium longum


text: public

text: Australia

text: Collinsella bouchesdurhonensis

text: Collinsella bouchesdurhonensis


text: public

text: Australia

text: Parafannyhessea umbonata

text: Parafannyhessea umbonata


text: public

text: Australia

text: Paraclostridium bifermentans

text: Paraclostridium bifermentans


text: public

text: Australia

text: Dorea longicatena

text: Dorea longicatena


text: public

text: Australia

text: Catenibacterium mitsuokai DSM 15897

text: Catenibacterium mitsuokai DSM 15897


text: public

text: Australia

text: Enterococcus faecalis

text: Enterococcus faecalis


text: public

text: Australia

text: Clostridium perfringens

text: Clostridium perfringens


text: public

text: Australia

text: Enterococcus faecium UC8668

text: Enterococcus faecium UC8668


text: public

text: Australia

text: Bacteroides caccae CL03T12C61

text: Bacteroides caccae CL03T12C61


text: public

text: Australia

text: Faecalicatena contorta

text: Faecalicatena contorta


text: public

text: Australia

text: Clostridium perfringens SM101

text: Clostridium perfringens SM101


text: public

text: Australia

text: Bifidobacterium adolescentis

text: Bifidobacterium adolescentis


text: public

text: Australia

text: Bifidobacterium longum subsp. longum JCM 1217


text: public

text: Australia

text: Lactococcus garvieae

text: Lactococcus garvieae


text: public

text: Australia

text: Bacteroides stercoris

text: Bacteroides stercoris


text: public

text: Australia

text: Escherichia coli IS25

text: Escherichia coli IS25


text: public

text: Australia

text: Bifidobacterium longum

text: Bifidobacterium longum


text: public

tag: Namespace:Institute of Botany, Czech Academy of Sciences

characteristic: altitude

text: B. Frajman and P. Schönswetter

text: Albania

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Poliçan, Mt. Tomorr, south of the southern summit, 6.3 km ENE of the village, alpine limestone scree

characteristic: geographic location (region and locality)

text: field

characteristic: growth facility

text: B. Frajman and P. Schönswetter

text: wild

characteristic: isolation and growth condition

text: Sabulina attica subsp. attica

text: Whole plant flowering stage (PO:0007016)

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: Phyllome (PO:0006001)

characteristic: plant structure

characteristic: ploidy

text: sexual

characteristic: propagation

text: healthy

characteristic: sample health state

text: Sabulina attica subsp. attica

characteristic: source material identifiers


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Institute of Botany, Czech Academy of Sciences

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: B. Frajman and P. Schönswetter

characteristic: collection date

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Papingo, Mt. Astraka NE of the village, limestone cliffs and screes

text: field

text: B. Frajman and P. Schönswetter

text: wild

text: Sabulina attica subsp. attica

characteristic: organism

text: soil

text: Phyllome (PO:0006001)

text: sexual

text: healthy

text: Sabulina attica subsp. attica

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: altitude

text: K. Nunvářová Kabátová and J. Chrtek

text: Greece

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Menalon ski center, 3.1 km NW of the village of Kardaras, alpine grassland, limestone

characteristic: geographic location (region and locality)

text: field

characteristic: growth facility

text: K. Nunvářová Kabátová and J. Chrtek

text: wild

characteristic: isolation and growth condition

text: Sabulina attica subsp. attica

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: Phyllome (PO:0006001)

characteristic: plant structure

text: sexual

text: healthy

text: Sabulina attica subsp. attica


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: A. Knotek

characteristic: collection date

text: Macedonia

text: Lubanista, near the road 6.2 km NE of the village, Paleozoic and Mezozoic carbonates

text: field

text: A. Knotek

text: wild

text: Sabulina attica subsp. attica

text: soil

text: Phyllome (PO:0006001)

characteristic: ploidy

text: sexual

characteristic: propagation

text: healthy

characteristic: sample health state

text: Sabulina attica subsp. attica

characteristic: source material identifiers


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: altitude

text: K. Nunvářová Kabátová and J. Chrtek

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: along a road 5 km W of the village of Tripi, calcareous rocks

characteristic: geographic location (region and locality)

text: field

characteristic: growth facility

text: K. Nunvářová Kabátová and J. Chrtek

text: wild

text: Sabulina attica subsp. attica

characteristic: organism

text: soil

text: Phyllome (PO:0006001)

text: sexual

text: healthy

text: Sabulina attica subsp. attica

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: K. Nunvářová Kabátová and J. Chrtek

characteristic: collection date

text: Greece

text: near a road close to Ekklisia Agii Apostoli 3.6 km NNW of the village of Ag. Nikolaos, silicates

text: field

text: K. Nunvářová Kabátová and J. Chrtek

text: wild

characteristic: isolation and growth condition

text: Sabulina attica subsp. attica

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: Phyllome (PO:0006001)

characteristic: plant structure

text: sexual

text: healthy

text: Sabulina attica subsp. attica


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: altitude

text: K. Nunvářová Kabátová and J. Chrtek

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Central Tzoumerka massif, SE slopes of Mt. Xerovouni (Pinakonili), above the road from Athamanio to Theodoriana, 2.5 km N of the village of Korakada, limestone rocks

text: field

text: K. Nunvářová Kabátová and J. Chrtek

text: wild

text: Sabulina attica subsp. attica

text: soil

text: Phyllome (PO:0006001)

characteristic: ploidy

text: sexual

characteristic: propagation

text: healthy

characteristic: sample health state

text: Sabulina attica subsp. attica

characteristic: source material identifiers


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: K. Nunvářová Kabátová and J. Chrtek

characteristic: collection date

text: Greece

text: slopes along the road between Elatos and Kalirachi, 1.7 km WSW of the village of Elatos, calcium-rich substrates,15 June 2015

characteristic: geographic location (region and locality)

text: field

characteristic: growth facility

text: K. Nunvářová Kabátová and J. Chrtek

text: wild

text: Sabulina attica subsp. attica

characteristic: organism

text: soil

text: Phyllome (PO:0006001)

text: sexual

text: healthy

text: Sabulina attica subsp. attica

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: altitude

text: K. Nunvářová Kabátová and J. Chrtek

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: ski center Vasilisa, ski slope S of the parking place, 3.2 km WSW of the village of Smix, silicate scree

text: field

text: K. Nunvářová Kabátová and J. Chrtek

text: wild

characteristic: isolation and growth condition

text: Sabulina attica subsp. attica

characteristic: plant developmental stage

text: soil

characteristic: plant growth medium

text: Phyllome (PO:0006001)

characteristic: plant structure

text: sexual

text: healthy

text: Sabulina attica subsp. attica


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: K. Nunvářová Kabátová and J. Chrtek

characteristic: collection date

text: Greece

text: Paggaio ski resort, 5 km SW of the village of Nikisiani, limestone

text: field

text: K. Nunvářová Kabátová and J. Chrtek

text: wild

text: Sabulina attica subsp. attica

text: soil

text: Phyllome (PO:0006001)

characteristic: ploidy

text: sexual

characteristic: propagation

text: healthy

characteristic: sample health state

text: Sabulina attica subsp. attica

characteristic: source material identifiers