Open Science Abbreviations

General Abbreviations

Abbreviation Definition

OSDR Open Science Data Repository

BDME Biological Data Management Environment

GL GeneLab

GLDS GeneLab Data Systems

ALSDA Ames Life Sciences Data Archive

NBISC NASA Biological Institutional Scientific Collection

RDSA Research Data Submission Agreement

Data Systems Abbreviations

Abbreviation Definition

MVP Minimum Viable Product

Sample OSDR Abbreviations

experiment to establish the initial condition of the experimental subjects

pFLT parabolic flight

pGC ground control for parabolic flight (i.e. samples were grown/processed in the same equipment as those in the pFLT groups)

soFLT suborbital ballistic rocket flight

soGC ground control for suborbital ballistic rocket flight (i.e. samples were grown/processed in the same equipment as those in the soFLT

groups)

CTRL control group for a space-relevant (but NOT spaceflight) experiment

HLU hind limb unloading (aka hindlimb suspension)

RL re-loaded - subjects re-exposed to limb/body loading

HLLC hind limb loaded control

TRHLLC tail restrained hind limb loaded control

uG microgravity

HG hypergravity http://bioportal.bioontology.org/ontologies/MESH?p=classes&conceptid=D018471

1G 1x gravity

2G 2x gravity

act activated

nonact non-activated

Tcells T cells

Dmel Drosophila melanogaster

Can-S Canton-Special (strain of Drosophila melanogaster)

Ecol Escherichia coli

Bbas Beauveria bassiana

infdw infected with

uninfd uninfected

sham-infd sham infected, treated similarly to the infected group but administered a control solution that does not contain an infectious agent (i.e.

treated with PBS, water, etc.)

Atha Arabidopsis thaliana

Brap Brassica rapa

nipp nipposinica (variant of Brassica rapa)

Etsl Etiolated seedlings - after further review I think “etiolation” should be made into standalone factor Kristen here - etiolation is a

condition of a sample we deal with differently now.

UdCC undifferentiated cell culture

BA1 BRIC A PDFU-1

BA2 BRIC A PDFU-2

BA3 BRIC A PDFU-3

BA4 BRIC A PDFU-4

BA5 BRIC A PDFU-5

BB2 BRIC B PDFU-2

BB3 BRIC B PDFU-3

BB4 BRIC B PDFU-4

BB5 BRIC B PDFU-5

BG1 BRIC G PDFU-1

BG2 BRIC G PDFU-2

BG3 BRIC G PDFU-3

WT wild-type

MUT mutant

wo whole organism

ADR Adrenal Glands

AT Adipose Tissue

BAT Brown Adipose Tissue

BRN Brain

Cb Cerebellum

CLN Colon

DSKN Dorsal Skin

EDL Extensor Digitorum Longus

eWAT Epididymal White Adipose Tissue

EYE Eye

FCS Feces

FSKN Femoral Skin

GST Gastrocnemius

HPC Hippocampus

iBAT Intrascapular Brown Adipose Tissue

iWAT Inginal White Adipose Tissue

KDN Kidney

LD Longissimus Dorsi Muscle

Lg-INT Large Intestines

LNG Lung

LVR Liver

HRT Heart

INT Intestines

MG Mammary Gland

OVY Ovary or Ovaries

Quad Quadricep

RTN Retina

SKN Skin

SLS Soleus

SM Skeletal Muscle

SPL Spleen

TA Tibialis Anterior

TES Testis or Testes

TMS Thymus

TNG Tongue

WAT White Adipose Tissue

RR Rodent Research

MHU Mouse Habitat Unit (JAXA mouse habitat unit)

FS Freezing Study

JAXA Japan Aerospace Exploration Agency

CC Cohort Control

C# Cohort Number

LAR Live Animal Return

ISS-T ISS Terminal Animal

NuRFB Nutrient Upgraded Rodent Food Bar

IR Irradiation

BSP Biospecimen Sharing Program

LSDA Life Science Data Archive

ALSDA Ames Life Science Data Archive

ACF Animal Care Facility

LLU Loma Linda University

KSC Kennedy Space Center

RNA Ribonucleic acid

DNA Deoxyribonucleic acid

PRT Protein

ALQ Aliquot

LN2 Liquid nitrogen

RNAlat RNA later

RIN RNA integrity number

DIN DNA integrity number

MIX1 ERCC Spike In mix 1

MIX2 ERCC Spike In mix 2

BLD Blood - we may want to revisit this - Whole Blood (WB), White Blood Cells (WBCs), Red Blood Cells (RBCs)

WB whole blood

WBCs White Blood Cells

RBCs Red Blood Cells

leu Leukocytes

L Left

Lg Large

R Right

D Dorsal

V Ventral

F Femoral

OD Optical Density

URR Universal Reference RNA

UHRR Universal Human Reference RNA

UMRR Universal Mouse Reference RNA

Gspe Genus species

C57-6J C57BL/6 mouse from Jackson Labs

OR Oregon R (Fruit Fly strain)

act2-3 Arabidopisis thaliana vegetative actin mutant

Col-0 Arabidopsis thaliana Columbia-0 ecotype

C57-10J C57BL/10J mouse from Jackson Labs

Ler-0 Landsberg ecotype

sShoots seedling shoots - will probably change. describes development AND anatomy. will review in JIRA process Amanda M. Saravia-butler

C57-6IBCh C57BL/6 mouse from Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russia

C57-6T C57BL/6 mouse from Taconic Biosciences

I dissected immediately after euthanasia

C dissected from frozen carcass

ARG1-KO A. thaliana Col-0 knock-out line deficient in the gene named Altered response to gravity-1

JkTcells Jurkat T cells

C57-6CR C57BL/6 mouse from Charles River

os-ind osteo-induced

not-ind not induced

BMSC Bone Marrow Stromal Cells

MSCs Mesenchymal Stem Cells

EMF treated with electromagnetic fields

suG simulated microgravity

LDC Large Diameter Centrifuge

RPoM Random Positioning Machine

ML Magnetic Levitator

do days old

yo years old

C Celsius

oLDC outside the Large Diameter Centrifuge

oRPoM outside the Random Positioning Machine

oML outside the Magnetic Levitator

YR Gamma Radiation

HZE High (H) Charge (Z) and Energy (E) HZE ionizing radiation

ATM1 mutant defective in the DSB-sensing protein kinase ATM

Gy Gray

sl seedling

sl-pool pool of 2 or more whole seedlings

lvCMC left ventricular cardiomyocytes

MCL medial collateral ligament

Rnor Rattus norvegicus

Sx surgery

noSx no surgery

shamSx sham surgery

bildisMCL bilateral disruption of the medial collateral ligament

lpup late pupae - may want to revisit. combining time/development and organism part

dT delta (change in) Temperature

NOdT no change in Temperature

ltdO2 limited Oxygen

normO2 normal Oxygen levels

Ws-0 Wassilewskija-0 (Arabidopsis thaliana) ecotype, species variant 391

Ws-2 Wassilewskija-2 (Arabidopsis thaliana) ecotype, species variant 393

Ws Wassilewskija (Arabidopsis thaliana) ecotype, species variant 382

Cvi-0 Cape Verde Islands - 0 (Arabidopsis thaliana) ecotype, species variant 98

suppO2 supplemented with Oxygen

kPa kilopascals

Hml-Gal4-UASGFP

Hemolectin-GAL4 crossed with UAS-GFP to make a transgenic line in Dmel

TKSC Tsukuba Space Center (JAXA)

N2 Bristol N2 (C.elegans strain)

Clinorotation Clinorotation

ISS International Space Station

RWV Rotating Wall Vessel

2T3cells osteoblast cell line 2T3

LS292 C.elegans strain representing a dys1(cx18) mutant

HF Hair Follicles

inFLT in spaceflight (describes condition in which sample was collected)

preFLT pre spaceflight (describes condition in which sample was collected)

postFLT post spaceflight (describes condition in which sample was collected)

BAL-SL BALB/c mouse from Simonsen Labs

BAL-JL BALB/c mouse from Jackson Laboratory

BAL-TAL BALB/c mouse from Taconic Animal Laboratory

4T1-Tumor Flank tumor derived from the 4T1 murine mammary carcinoma cell line that was generated from a BALB/cfC3H mouse

1D11 Antibody that binds to TGFB and thus inhibits function

IsoCTRL Isotype control - primary antibodies that lack specificity to the target, but match the class and type of the primary antibody used in the

application

TGFB-Het TGFBeta-Heterozygote

Sham type of control sample

post-Sham describes sample post sham

post-IR describes sample post irradiation

wk week (Time)

LCL Lymphoblastoid Cell Line Amanda M. Saravia-butler i have a dataset we could test this on. Lets revisit this one

GM15036 Lymphoblastoid Cell Line GM15036

GM15510 Lymphoblastoid Cell Line GM15510

RCCS Rotary Cell Culture System

RAW2647cells RAW 264.7 cell line

TK6cells TK6 Lymphoblast Cell Line

cax1-1 describes cax1-1 transgenic line of Arabidopsis thaliana

SDR Sprague Dawley Rats (for general use when source is not available Amanda M. Saravia-butler )

SDR-TF Sprague Dawley Rats from Taconic Farms

56Fe Iron isotope

C3H-He-Slc C3H/He mice from Japan Slc, Inc.

C57-6J-Jms-

Slc

C57BL/6J Jms mice from Japan Slc, Inc.

AJ-Jms-Slc A/J Jms mice from Japan Slc, Inc

h hour (Time)

Cs137 Caesium-137 isotope

Epi200MT 3-dimensional tissue model of human epidermis, MatTek Corporation, Ashland, MA

SMK Smoker - not to be confused with Super Mario Kart

nSMK non-Smoker

um micrometer

tumor tumor

MCF10Acells MCF10A cells - human mammary epithelial cells

TGFB Tumor Growth Factor Beta

X-ray X-ray irradiation

Preg Pregnant

Lac Lactating

Hi-LET High Linear Energy Transfer

Si Silicon isotope

C3H-HeJ C3H Heston mouse from Jackson Labs (aka C3H/HeJ)

d day (time)

K-12MG1655 strain (of E. coli) K-12 MG1655

HBF hyper-buoyancy flotation (used for bed-rest study)

VL vastus lateralis

Rep replicate

Hsap Homo sapiens

Mmus Mus musculus

shamIR mock irradiation (i.e. subject to irradiation equipment but not exposed to irradiation)

HUVEC Cells derived from the endothelium of veins from the umbilical cord

Scer Saccharomyces cerevisiae

BY4742 Strain of Saccharomyces cerevisiae

BY4742_FLO1 S. cerevisiae strain BY4742 over-expressing the FLO1 member of the Flo adhesin protein family

BY4742_FLO8 S. cerevisiae strain BY4742 over-expressing the FLO8 member of the Flo adhesin protein family

Cele Caenorhabditis elegans

BMCs bone marrow cells

BM bone marrow

Euth Euthasol

DI Dry Ice

Ket-Xyl Ketamine/Xylazine

ext1 RNA was extracted the same day organs were dissected from frozen carcasses

ext2 Organs were dissected from frozen carcasses, flash frozen in (l)N2 and stored at -80C then RNA was extracted on a later date

Lminus Launch minus (usually followed by a time frame, for example Lminus30d means 30 days before launch)

Lplus Launch plus (usually followed by a time frame, for example Lplus30d means 30 days after launch)

Rminus Return minus (usually followed by a time frame, for example Rminus30d means 30 days before return to earth)

Rplus Return plus (usually followed by a time frame, for example Rplus30d means 30 days after return to earth)

CO2 Carbon Dioxide

RLT RNeasy Lysis Buffer

IRC Irradiation Control - No mock IR was performed, i.e. subjects were not exposed to IR nor an IR set-up

F# mouse number from a spaceflight group

G# mouse number from a ground control group

B# mouse number from a basal group

V# mouse number from a vivarium group

R1 Forward Read

R2 Reverse Read

JC JAXA Chow

JCwFOS JAXA Chow fortified with fructooligosaccharides (FOS)

Alight specimen grown in Ambient light

dark specimen grown in darkness

Col-0-PhyD Columbia ecotype with a mutation in phytochrome D (PhyD)

mon month

y year(s)

SP spleen pool - spleens from 2 or more animals pooled together to make one sample

ss-tissues tissues that underwent size selection during library prep (after extraction)

tissues more than 1 tissue from 1 animal was pooled

MCC MidiCAR centrifuge

MgSO4 magnesium sulfate

min minute

Rotation rotation

Hypocotyl hypocotyl

HypocotylCC Hypocotyl cell culture (a cell culture derived from the hypocotyl part of the plant)

PBLD Peripheral Blood

In-FLT-CTRL In-flight Control

PC pipette centrifuge

Olat Oryzias latipes

TGFP-ODsRed Oryzias latipes (Japanese medaka) F1 fish of two closed colonies; Japanese medaka wild type Cab and Cab strain transgenic fish

(TRAP:GFP, Osterix:DsRed)

NCTC-86 strain (of E. coli) NCTC 86; ATCC 4157

ug-mL concentration in micrograms per milliliter

Smut Streptococcus mutans

ITS internal transcribed spacer

Paer Pseudomonas aeruginosa

RWV-V Rotating Wall Vessel in veritical direction

RWV-H Rotating Wall Vessel in horizontal direction

PA01 PAO1 strain - Pseudomonas aeruginosa

HMVEC-dBL Human dermal microvascular endothelial cells

LPS lipopolysaccharide

S-UHRR Stratagene Universal Human Reference RNA

PTN-OSF1 transgenic mice overexpressing the osteogneic factor PTN/OSF1

cells material type - cell line

DLD-1 DLD-1 cells epithelial, adherent cell line derived from a colorectal adenocarcinoma (Dukes type C)

MOLT-4 MOLT-4 cell line T lymphoblast, suspension cell line derived from an acute lymphoblastic leukemia

IMR90iPSCs induced pluripotent stem cells derived from the IMR90 human cell line

CPCs Cardiac progenitor cells

PhaB Pharyngeal Bones

Cab wild type Cab strain of Oryzias latipes (Japanese medaka fish)

LC Laboratory control - may refer to a control group or groups grown under standard laboratory conditions and processed to test an

aspect(s) of spaceflight experimental parameters

TLCs T lymphocyte cells

cGy centigray

168 Strain of Bacillus subtilis

PBMCs peripheral blood mononuclear cells

pip2Dclino 2D pipette clinostat

pipcent pipette centrifuge

ALLCL acute lymphoblastic leukemia cell line

CRCCL colorectal cancer cell line

GF Glovebox Freezer

CyroC Cyrochiller

WCar Whole Carcass (i.e. the sample was extracted from an intact carcass)

PCar Partial Carcass (i.e. the samples was extracted from a carcass that had one or more part(s) removed)

Esco Euprymna scolopes

aposym aposymbiotic

sym symbiotic

HARV high-aspect-ratio rotating wall vessel bioreactors

LO Light Organ

UAMS-1 Strain of Staphylococcus aureus

Saur Staphylococcus aureus

Mmar Mycobacterium marinum

LHM4 Strain of Mycobacterium marinum

InsP-5-ptase transgenic Arabidopsis thaliana (Columbia-0) plants constitutively express the mammalian type I inositol polyphosphate 5-

phosphatase (InsP 5-ptase)

LLC Lewis lung carcinoma

LLCtumor Tumor derived from Lewis lung carcinoma cells

LLCcells Lewis lung carcinoma cells

Trp53N-MG Trp53 null mammary gland

B6.

129S2KrasLA1

B6.129S2-Krastm2Tyj/Nci Mouse strain - This strain carries a targeted latent ‘hit-and-run’ K-ras allele that can be activated by an in

vivo spontaneous recombination event (‘run’). One half of the in vivo recombination events result in a normal K-ras allele and one half

in an activated allele (K-rasG12D).

Trp53N-MGT Trp53 null mammary gland tumor

Drer Danio rerio

PBLs peripheral blood lymphocytes

AG01522 human fibroblasts AG01522 cells

ble bleomycin

FBC fibroblasts cells

Low-LET Low Linear Energy Transfer

C57-6 C57BL/6 mouse from an unknown origin

cls plant callus

T tesla (magnetic field unit)

MM2d Arabidopsis thaliana MM2d cell line

Bsub Bacillus subtilis

S288C strain of Saccharomyces cerevisiae

HIR Heavy Ion Radiation

TNR Thermal Neutron Radiation

FNR Fast Neutron Radiation

HSFA2-KO a knockout Arabidopsis thaliana line deficient in the gene encoding HSFA2

AB Strain of Danio rerio

WN624 Strain of Bacillus subtilis

WN1106 Strain of Bacillus subtilis

HEBC3KT a human bronchial epithelial cell line

28Si Si 28 isotope

Zone-I region of root apex: 0.5 mm, root cap and meristematic zone

Zone-II region of root apex: 1.5 mm, transition, elongation and growth terminating zone

Node3 node 3 of ISS

AHSFS air handling system filter screen of ISS

SIEV sieved

Batr Bacillus atrophaeus

blank no DNA or RNA added to extraction kit

PAS passive aerosol sample

HBECs human bronchial epithelial cells

2D cells grown in 2D condition

3D cells grown in 3D condition

TT tetanus toxoid (treatment with tetanus toxoid)

noTT tetanus toxoid control (animals were not treated with tetanus toxoid, just the solution used to dilute the tetanus toxoid)

ODNCpG adjuvant treatment of a synthetic oligodeoxynucleotide (ODN) containing unmethylated CpG motifs (CpG)

noODNCpG adjuvant treatment control (animals were not treated with ODNCpG, just the solution used to dilute the ODNCpG)

AG1522 a normal human foreskin fibroblast cell line

HT1080 a human fibrosarcoma cell line

RAD51 RAD51 gene

G1 G1 phase of cell cycle

G2 G2 phase of cell cycle

Asyn Asynchronous cells, cells in various phases of cell cycle

FirstSet first set of animals (or samples) processed/preserved in a given day of operations

SecondSet second set of animals (or samples) processed/preserved in a given day of operations

ThirdSet third set of animals (or samples) processed/preserved in a given day of operations

FourthSet fourth set of animals (or samples) processed/preserved in a given day of operations

CTRLSet control set of animals (or samples) processed/preserved in a given day of operations

Styp Salmonella typhimurium

SL1344 Salmonella enterica subsp. enterica serovar Typhimurium strain SL1344

dhfq isogenic hfq deletion mutant

HT-29 human colorectal adenocarcinoma cell line with epithelial morphology

U937 human macrophage cell line established from a diffuse histiocytic lymphoma

3DCoC 3D co-culture model

LoopG Loop Genomics

w1118 strain of Drosophila melanogaster

16S 16S rRNA gene

DFVS dust filter of ventilation system

VAC vacuum

INCd incubated

arch archaea

uni universal

M# mouse number

S# subject number

scWim sample collected while inside module

scAem sample collected after exiting module

scBem sample collected before entering module

SKF ion channel inhibitor SKF-96365

HRremoved Human Reads removed

Heat samples treated with heat

noHeat samples not treated with head

Anox Anoxia (oxygen deprived)

noAnox not Anoxia (not oxygen deprived)

mid-age middle-age

C57-6NIA C57BL/6 mouse from National Institute of Aging

CUMS chronic unpredictable mild stressors

Eves Eruca vesicaria

CAAT Controlled Artificial Ageing Treatment

cop1 cop1 gene

uvr8 uvr8 gene

PWB partial weight bearing, as with a harness to reduce loading on all limbs - usually followed by a value for the % of loading. Ex: PWB40

= 40% of normal loading; PWB100 = 100% of loading (or loading control)

FEM femur

TRIB triceps brachii

CVA calvaria