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text: Protocols: EpiSCs were seeded at ~6 × 103 cells/cm2 in six-well cell-culture plates pre-coated with 15 µg/ml human Fibronectin, and differentiated to PS as described in the article. At desired time-points, cells were dissociated using Accutase (Thermo Fisher Scientific, 00-4555-56) for 3 min at 37 °C and counted. 500,000 cells per condition were washed with ice-cold FACS buffer (10% (v/v) FBS in PBS) and resuspended into 1 ml ice-cold FACS buffer containing 1 µg/ml DAPI.Cells were washed with 500 μl ice-cold FACS buffer, centrifuged again at 350 × g for 3 min and resuspended into 250 μl ice-cold FACS buffer containing 1 µg/ml DAPI. Singlecells from in vitro-differentiated cells were sorted into Eppendorf Polypropylene U-shaped 384-well Twin Tec PCR Microplates (Thermo Fisher Scientific, 10573035), containing 2 μl of lysis solution (0.2% (v/v) Triton X-100) supplemented with 0.4 U/μl RNasin Ribonuclease Inhibitor (Promega, N2515) and 400 nM indexed RT primer from group 1 (1-96 barcodes) or group 2 (97-192 barcodes) Cells were washed with 500 μl ice-cold FACS buffer, centrifuged again at 350 × g for 3 min and resuspended into 250 μl ice-cold FACS buffer containing 1 µg/ml DAPI. Singlecells from in vitro-differentiated cells were sorted into Eppendorf Polypropylene U-shaped 384-well Twin Tec PCR Microplates (Thermo Fisher Scientific, 10573035), containing 2 μl of lysis solution (0.2% (v/v) Triton X-100) supplemented with 0.4 U/μl RNasin Ribonuclease Inhibitor (Promega, N2515) and 400 nM indexed RT primer from group 1 (1-96 barcodes) or group 2 (97-192 barcodes). Additionally, 71 WT EpiSCs were sorted into each plate, as spike-in control for batch-effect correction. Capture plates were prepared on the Bravo automated liquid handling robot station (Agilent) using 384-filtered tips (Agilent, 19133-142). Index sorting was performed using a FACS Aria III cell sorter (BD Biosciences) at the DanStem Flow Cytometry Platform (University of Copenhagen, Copenhagen, Denmark), sorting live cells as singlets. Immediately after sorting, plates were spun down, snap-frozen on dry ice and stored at −80 °C until further processing. Semi-automated library preparation was performed, using 10-12 total cycles of PCR amplification and AMPure XP beads (Beckman Coulter Life Sciences, A63881) for purification63. DNA concentration was measured with a Qubit Fluorometer (Thermo Fisher Scientific, Q32854) and fragment size was determined with a Fragment analyzer (Agilent).

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text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: ExM cell 367

characteristic: single cell identifier


text: public

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: ExM cell 368


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

characteristic: organism part

text: pluripotent stem cell

text: Mus musculus

text: ExM cell 369


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

characteristic: progenitor cell type

text: Mus musculus

text: ExM cell 370


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

characteristic: common name

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: ExM cell 371

characteristic: title


text: public

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: ExM cell 372

characteristic: single cell identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: ExM cell 373


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

characteristic: organism part

text: pluripotent stem cell

text: Mus musculus

text: ExM cell 374


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

characteristic: common name

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

characteristic: progenitor cell type

text: Mus musculus

text: ExM cell 375


text: public

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: ExM cell 376

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: ExM cell 377

characteristic: single cell identifier


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: ExM cell 378


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

characteristic: common name

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

characteristic: organism part

text: pluripotent stem cell

text: Mus musculus

text: ExM cell 379


text: public

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

characteristic: description

text: embryo

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

characteristic: progenitor cell type

text: Mus musculus

text: ExM cell 380


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: ExM cell 381

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: epiblast stem cells

text: extraembryonic mesoderm

text: house mouse

text: embryo

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: epiblast

text: pluripotent stem cell

text: Mus musculus

text: ExM cell 382

characteristic: single cell identifier


text: Ragimbeau

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: DNA from synthetic mixture of C.jejuni strains

text: Campylobacter jejuni

characteristic: organism

text: Campylobacter jejuni


text: public

tag: Namespace:Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS)

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: human

characteristic: common name

text: Protocols: A549 cells were maintained in Gibco DMEM/F12 medium supplemented with GlutaMAX and 10% FBS at 37°C with 5% CO2. Cells were mock infected or infected with influenza A/Puerto Rico/8/1934 virus (from the collection of Smorodintsev Research Institute of Influenza, Ministry of Health of the Russian Federation) at a dose of 1 TID50/cell and incubated at 37°С for 24 h or 48 h. In this study influenza A/Puerto Rico/8/1934 was used to infect A549 cells. Mock-infected cells were included at analysis as control. Following the incubation period, the cell monolayer was washed twice with PBS and was directly lysed by adding phenol-containing LIRA reagent (Biolabmix, Russia). Small RNA (<200 nucleotide length) was extracted from cells using phenol/chloroform extraction with LRU RNA extraction kit (Biolabmix, Russia) according the manufacturer’s protocol and analyzed on a 1.5% TAE-agarose gel and using Bioanalyzer 2100 instrument (Agilent, USA) with an Agilent Small RNA kit. The quality of the Input RNA was assessed by the Agilent Bioanalyzer 2100 System and Agilent Small RNA kit (Agilent, USA). ~0.5 µg of enriched small RNA (<200 nucleotide length) was used for library construction. The construction of cDNA libraries according to a standard protocol using a NEBNext Multiplex Small RNA Library Prep Kit for Illumina (New England Biolabs, UK), as well as massive parallel sequencing on a NextSeq Illumina 500 platform, were conducted at the Institute of Fundamental Medicine and Biology, Kazan Federal University (Kazan, Russia). Libraries concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system using Qubit DNA HS Assay Kit (Thermo Fisher Scientific). The quality control analysis of libraries was assessed using the Agilent Bioanalyzer 2100 System and DNA High Sensitivity Chip (Agilent, USA).

characteristic: description

text: adult

characteristic: developmental stage

text: adenocarcinoma

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: lung epithelium

characteristic: organism part

characteristic: replicate

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS)

text: public

text: ArrayExpress

text: epithelial cell

text: human

text: adult

text: adenocarcinoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: lung epithelium

text: Homo sapiens

text: male

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Laboratoire de Developpement des Gonades Universite Paris Cite CEA Universite Paris-Saclay,

characteristic: Submitter Id

text: ArrayExpress

text: iPSC derived cell line

text: embryonic stem cell

text: human

text: Protocols: Naive human induced pluripotent stem cell (hiPSC) (PB12.CO3: 46XX) were plated in ultra-low attachment U-bottom 96 well plates at a density of 8 000 to 10 000 cells/well in a PGC-LC medium. This latter was composed of Glasgow’s Minimal Essential Medium (GMEM, GIBCO), 15% KSR (GIBCO), 0.1 mM nonessential amino acids (GIBCO), 0.1 mM 2-mercaptoethanol (GIBCO), 100 U/ml Penicillin- 100 U/ml Streptomycin (GIBCO), 2 mM L-Glutamine, 1 mM Sodium pyruvate (Sigma), and the following cytokines: 500 ng/ml BMP4 (Peprotech), 1 µg/ml human LIF (Peprotech), 100 ng/ml SCF (Peprotech), 50 ng/ml EGF (Peprotech), and 10 µM ROCK inhibitor. To force embryoid body aggregation, cells were centrifuged at 200 g for 2 min and cultured for 4 days. Around 60 embryoid bodies by sample were dissociated and stained with Hoescht 33258. Single-cell suspensions from EB at day 4 were pooled before Hoescht 33258 staining. Total viable cells were flow-sorted into PBS-BSA 0.05%. Sorted cells were centrifuged and counted, and 4,000 cells were loaded onto the Chromium 3′ chip. Two replicates (EBD4_A, EBD4_B) from two different pools of EBd4 were encapsulated independently. Cells capture, lysis & RNA extraction were performed using the 10x V3 Chromium technology as recommended by the manufacturer. Around 4,000 cells by replicate were loaded in each lane of the Chromium 3′chip. Barcoding and library preparation were performed with the 10x Chromium system using version 3 chemistry (Dual index TT_C4 for EBD4_A and TT_C4 for EBD4-B) ), following the manufacturer’s protocol. cDNA was synthesized and amplified as per manufacturer’s protocol and amplified to construct an Illumina sequencing library. cDNA and libraries were checked for quality on using Agilent with DNA HS chip..

text: adult

text: normal

text: wild type genotype

text: embryoid body culture

characteristic: growth condition

text: pool of around 60 embryoid bodies

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: induced pluripotent stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: female


text: Laboratoire de Developpement des Gonades Universite Paris Cite CEA Universite Paris-Saclay,

text: public

text: ArrayExpress

characteristic: broker name

text: iPSC derived cell line

text: embryonic stem cell

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

text: embryoid body culture

text: pool of around 60 embryoid bodies

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: induced pluripotent stem cell

characteristic: replicate

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:INSERM U1151-Institut Necker-Enfants malades

text: ArrayExpress

text: B cell

text: human

text: Protocols: PBMCs from blood of healthy donors that was collected before and after Pneumovax vaccination, were isolated by centrifugation on Ficoll-Paque PLUS (GE Healthcare) and were stained with the following anti-human antibodies: APC-H7 anti-CD3/CD14/CD16, V500 anti-CD19, APC anti-CD27, PerCPcy5.5 anti-CD38, PE-Cy7 anti-CD24, Pe-Cy7 anti-IgD and FITC-CD43. All the mAbs were from BD Biosciences, except the anti-CD24 mAb (SONY) and the anti-IgM mAb (Biolegend). Dead cells were excluded by Sytox Blue staining (Invitrogen). Lymphocytes were first gated based on morphology, before exclusion of doublets, dead cells and CD3/CD14/CD16-positive cells. The sorted fractions and their phenotypes were as following : - plasmacells or \PC\ (CD19+CD27++CD38++)- \MZB\ cells (CD19+CD43-CD38lowCD27+IgM+IgD+)-switched memory cells or \SM\ (that encompasses switched and IgM-only cells (CD19+CD43-CD38lowCD27+IgD-)- double negative or \DN\ (CD19+CD43-CD38lowCD27-IgD-)-\naives\ B cells (CD19+CD43-CD38lowCD27-IgM+IgD+ The B cell fractions were sorted using a FACSAria III cell sorter (BD Biosciences) and were collected in Eppendorf tubes filled with PBS+ 2% fetal calf serum. After a centrifugation step and supernatant removal, the cell pellets were resuspended into 75 μl of RT lysis buffer (RNeasy Kit, Qiagen) and either frozen at -80°C or directly subjected to RNA extraction RNA extraction of the sorted cell fractions was done with the mini- or micro-RNeasy kit, according to the manufacturer’s instructions. Starting from a maximum of 150 ng of total RNA, mRNAs were then isolated with Dynabeads oligo (dT) from Thermo Fischer Scientific, according to the manufacturer’s guidelines and immediately used in their entirety for reverse transcription in solid phase according to a protocol adapted from Vergani et al, Frontiers in Immunology 8 (2017) with modified NGS primers (see sup. Table 5 , doi: https://doi.org/10.1101/833343). cDNA was synthetized in 10 μl (50°C for 1 hour and 72°C for 10 min) using SuperScript III Enzyme (Thermo Fisher Scientific). After ribonuclease H treatment (Clontech Takara) second-strand synthesis was performed in solid phase in 10 μl using Q5 Polymerase (New England Biolabs) and a mix of 13 primers covering IGHV leader sequences, containing 13 to 16 random nucleotide (UMI) and partial Illumina adaptor sequences (37°C for 20 min, 98°C for 30 s, 62°C for 2 min, and 72°C for 10 min). IGHV-D-J-CH double-stranded cDNA attached to the magnetic Dynabeads was washed three times in 10 mM Tris-HCl (pH 8.0) to remove the remaining primers, and the entire sample was used as a template for the PCR1 amplification in 10 μl using Q5 Polymerase with a forward primer that is specific for the partial Illumina adaptor sequence and allowing its extension, and a mix of reverse isotype specific (μ, α, and γ) primers (98°C for 30 s; 10 cycles of 98°C for 10 s, 58°C for 15 s, and 72°C for 1 min; 72°C for 10 min). Depending on the initial cell fraction, individual semi-nested PCR2 were performed with inner reverse primers specific for the mu, alpha, or gamma constant region and allowing the introduction of partial Illumina adaptors. Two microliters of the PCR1 product was used for the semi-nested PCR2 reactions carried in 20 μl (98°C for 30 s; 15 cycles of 98°C for 10 s, 58°C for 15 s, and 72°C for >1 min; 72°C for 10 min). The PCR2 products were purified with AMPure I XP beads at a ratio of 1:1, and 1 to 10 ng was used to add Illumina Index with the Nextera XT kit (Illumina). After a final purification with AMPure XP beads (ratio 1:1), the library obtained for each sample was diluted at a concentration of 2 nM and pooled equimolarly into a final pool. Sequencing was performed with the Illumina MiSeq sequencer using the V3 kit (2 × 300) with 12 pmol of the final pool and 10% PhiX control to avoid low-complexity library issues.

text: adult

text: normal

characteristic: disease

characteristic: immunophenotype

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male

characteristic: title


text: INSERM U1151-Institut Necker-Enfants malades

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: B cell

text: human

text: adult

text: normal

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: Homo sapiens

text: male


text: Jin Li

text: public

tag: Namespace:Jin Li

text: human embryonic stem cells

text: human

characteristic: common name

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: strain

text: human embryonic


DAPT

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Jin Li

text: public

text: DAPT

text: human embryonic stem cells

text: human

text: Homo sapiens

text: Homo sapiens

text: human embryonic

text: DAPT


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Lubeck

text: public

tag: Namespace:University of Lubeck

characteristic: Time

characteristic: Tube

text: human

text: stool

text: microbiome

characteristic: environmental package

characteristic: id

text: Homo sapiens

text: Homo sapiens

text: MiSeq

characteristic: sequencing method


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Institute of Genetic Medicine Newcastle University

text: human

text: leuk. cell line

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: Institute of Genetic Medicine Newcastle University

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

characteristic: common name

text: leuk. cell line

characteristic: description

text: Homo sapiens

text: Homo sapiens