Table 1 Sample type, processing details and storage characteristics of maternal and neonatal specimens

Maternal blood^a

 ● SST × 1

 ● EDTA × 2

 ● PaxGene × 1

Umbilical cord blood^a

 ● SST × 1

 ● EDTA tube × 2

 ● PaxGene tube × 1

Neonatal blood^b

 ● EDTA microtainer × 2

Serum

SST tube spun at 1200 g × 10 min at RT, aliquoted into cryovials

Plasma

EDTA tube spun at 1000 g × 10 min at RT, aliquoted in cryovials

Ficoll-based PBMC isolation

Following plasma removal, remainder of blood diluted with 1:1 HBSS, layered on top of Ficoll at 2:1 ratio, spun at 1000 g at 30 min; PBMC layer collected, diluted in HBSS for counting

Granulocyte/neutrophil isolation

Isolated using EasySep Direct Human Neutrophil Isolation Kit (StemCell Technologies) for subsequent RNA or DNA analysis

PaxGene

Shaken vigorously at time of collection, store at RT for at least 2 h

Serum

− 80 °C

Plasma

− 80 °C

PBMCs

Suspended in freezing medium at − 80 °C × 24 h, then transferred to liquid nitrogen for long term storage

Granulocytes/neutrophils

RNA: Resuspended at 1 × 105 cells/tube in Buffer TCL (Qiagen) and 1% BME

DNA: Pelleted at 5 × 106 cells/tube and stored

PaxGene

Collection tube stored in

− 20 °C overnight, then transferred to − 80 °C

Saliva^a

Sputum^a

Mixed 1:1 with DTT and aliquoted

−80 °C

Nasal swab^a

Nasopharyngeal swab^b

Oropharyngeal swab^{a, b}

Collected in PBS, stored immediately at 4 °C after collection, processed within 3–4 h; PBS collection media aliquoted

−80 °C

Vaginal swab^a

Rectal swab^a

Stored immediately at 4 °C after collection; stalk removed, swab tip placed in cryovial and stored within 3–4 h of collection

−80 °C

Urine^{a, b}

Maternal urine aliquoted into cryovials

Neonatal urine-soaked cotton balls from newborns transferred to 60 mL syringe to dispense urine; aliquoted into cryovials

−80 °C

Placenta^a

Biopsies for RNA analysis

2 x 5mm³ biopsies collected from maternal side and fetal side immediately after delivery, washed in PBS × 2, stored upright in RNAlater at 4 °C × 24 h.

Sections for histopathology

Full thickness placental sections fixed in formalin and paraffin-embedded into blocks for in situ histopathology

Biopsies for RNA analysis

Biopsies divided into ~ 50 mg pieces and snap frozen in liquid nitrogen, then stored at − 80 °C

Sections for histopathology

RT

Stool^{a, b}

Microspatula used to dispense ~ 1 cc into 1 mL RNAlater, empty cryovials, or 1 mL Buffered Glycerol Saline (Fisher)

−80 °C

Breastmilk^a

Stored at 4 °C after collection, milk collection tube rewarmed in hands briefly emulsify lipids then aliquoted into cryovials within 3–4 h of collection

−80 °C

Tracheal aspirates^b

Resuspended in trizol and aliquoted into cryovials

−80 °C