OSDR Tutorials
How-To Guides
Access Data in the Open Science Data Repository (OSDR)
Searching for data within the OSDR
General Search Filters
Data Source
Data Type
Study Search Filters
Example Search
Navigate an OSDR Study Page
Navigation panel
Study Overview: OSD ID, Title, GeneLab ID, ALSDA ID and DOI
Description: Factor(s), organism, assay(s), project and contact information.
Experiments
Payloads
Missions
Protocols
Samples
Selecting sample(s) metadata for export
Assays
Selecting assay metadata for export
Publications
Files
Version History
Visualization
Request Controlled Access Datasets from OSDR
Step 1: Identify the Dataset
Step 2: Investigator Submits Data Access Request (DAR)
Step 3: Verify Affiliation
Step 4: Request Reviewed by OSDR Curation Team
Step 5: Data Access Committee Reviews Request
Step 6: Access Data
Step 7: Report Progress
Step 8: Close Out
Step 9: Questions?
Use the OSDR Public AWS S3 Bucket
Getting Started with AWS and OSDR Data
Introduction to OSDR Data on AWS
Installing the AWS CLI
Exploring OSDR Data
Copying Data Locally
Additional Resources
Create a Login.gov Account
Step 1: Sign Up
Step 2: Verify Email
Step 3: Set Password
Step 4: Registration Complete
Step 5: Log In
Step 6: Select ‘Submission Portal’ or ‘Workspace’
Step 7: BDME Dashboard (Submission Portal)
Step 8: Access the Workspace
Troubleshooting Steps
Use the OSDR Workspace
The OSDR Workspace
Workspace Console
Add New Folder
Download Files
Data Submission Guide
Prior to starting the data submission process please do the following:
Data Submission Tutorial
Download and Complete the Sample Metadata Files
Download and Complete the Assay Metadata Files
Create a Login.gov Account and Upload Files to Workspace
Login to BDME and Create a New Study
Input Study Information, Sample and Assay Metadata, and Associate Data Files
Preview Your Study and Submit to OSDR
Use the Biological Data API
The ISA model
Hierarchical metadata in the Biological Data API
Additional fields
Query endpoints vs. REST endpoints
Obtaining metadata tables
Obtaining data tables
Output formats
Explore Data Visualizations
About Data Visualization
Metadata Dashboard
Filters
Studies Table
Single Study Visualization Portal
Sidebar Functions
Plotly
PCA Plots
Pair Plots
Volcano Plots
Heatmap
DGE Table
GSEA
Ideogram
Multi-Study
Exploring the Multi-Study Page
Multi-Study PCA Plot
Factor Selection for Gene Expression Analysis
Sample Selection for Gene Expression Analysis
Normalize Using Only Selected Samples and/or Factors
Visualizing and Downloading Results
Exploring Visualization Plots
View and Download Environmental Data
Telemetry data
Radiation data
Mission comparison
Data Tables
Use the RadLab Portal and Data API
Data Overview Page
RadLab Time Series Line Plots
Data Comparison
Geospatial Plots
Knowledgebase
Data API
Settings
Report Issues to OSDR
Visit the OSDR Contact Page
Complete the Contact OSDR Form
Portals
Data Repository
Data Visualization Portal
EDA
RadLab
Explore NBISC
GitHub Repos
OSDR Curation
GeneLab Sample Processing
GeneLab Data Processing
Reference
Open Science Abbreviations
General Abbreviations
Data Systems Abbreviations
Sample Abbreviations
OSDR Tutorials
Index
Edit on GitHub
Index
Symbols
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A
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B
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C
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D
|
E
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F
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G
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H
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I
|
J
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K
|
L
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M
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N
|
O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
|
Y
|
Z
Symbols
168
16S
1D11
1G
28Si
2D
2G
2T3cells
3D
3DCoC
4T1-Tumor
56Fe
A
AB
ACF
act
act2-3
ADR
AG01522
AG1522
AHSFS
AJ-Jms-Slc
Alight
ALLCL
ALQ
ALSDA
Anox
aposym
arch
ARG1-KO
Asyn
AT
Atha
ATM1
AWG
B
B#
B6.129S2KrasLA1
BA1
BA2
BA3
BA4
BA5
BAL-JL
BAL-SL
BAL-TAL
BAT
Batr
BB2
BB3
BB4
BB5
Bbas
BDME
BG1
BG2
BG3
bildisMCL
blank
BLD
ble
BM
BMCs
BMSC
Brap
BRN
BSL
BSP
Bsub
BY4742
BY4742_FLO1
BY4742_FLO8
C
C
C#
C3H-He-Slc
C3H-HeJ
C57-10J
C57-6
C57-6CR
C57-6IBCh
C57-6J
C57-6J-Jms-Slc
C57-6NIA
C57-6T
CAAT
Cab
Can-S
cax1-1
Cb
CC
CEC
Cele
cells
cGy
Clinorotation
CLN
cls
CO2
Col-0
Col-0-PhyD
cop1
CPCs
CRCCL
Cs137
CTRL
CTRLSet
CUMS
CVA
Cvi-0
CyroC
D
D
d
DAR
dark
DFVS
dhfq
DI
DIN
DLD-1
Dmel
DNA
do
Drer
DSKN
dT
E
Ecol
EDL
EMF
Epi200MT
Esco
Etsl
Euth
Eves
eWAT
ext1
ext2
EYE
F
F
F#
FBC
FCS
FEM
FirstSet
FLT
FNR
FourthSet
FS
FSKN
G
G#
G1
G2
GC
GF
GIS
GL
GLDS
GM15036
GM15510
Gspe
GST
Gy
H
h
HARV
HBECs
HBF
Heat
HEBC3KT
HF
HG
Hi-LET
HIR
HLLC
HLU
Hml-Gal4-UAS-GFP
HMVEC-dBL
HPC
HRremoved
HRT
Hsap
HSFA2-KO
HT-29
HT1080
HUVEC
Hypocotyl
HypocotylCC
HZE
I
I
iBAT
IMR90iPSCs
In-FLT-CTRL
INCd
infdw
inFLT
InsP-5-ptase
INT
IR
IRC
IsoCTRL
ISS
ISS-T
ITS
iWAT
J
JAXA
JC
JCwFOS
JkTcells
K
K-12MG1655
KDN
Ket-Xyl
kPa
KSC
L
L
Lac
LAR
LC
LCL
LD
LDC
Ler-0
leu
Lg
Lg-INT
LHM4
LLC
LLCcells
LLCtumor
LLU
Lminus
LN2
LNG
LO
LoopG
Low-LET
Lplus
LPS
lpup
LS292
LSDA
LSDS
ltdO2
lvCMC
LVR
M
M#
MCC
MCF10Acells
MCL
MG
MgSO4
MHU
mid-age
min
MIX1
MIX2
ML
MM2d
Mmar
Mmus
MOLT-4
mon
MSCs
MUT
MVP
N
N2
NBISC
NCTC-86
nipp
noAnox
Node3
NOdT
noHeat
nonact
noODNCpG
normO2
noSx
not-ind
noTT
nSMK
NuRFB
O
OD
ODNCpG
Olat
oLDC
oML
OR
oRPoM
os-ind
OSD
OSDR
OVY
P
PA01
Paer
PAS
PBLD
PBLs
PBMCs
PC
PCar
pFLT
pGC
PhaB
pip2Dclino
pipcent
post-IR
post-Sham
postFLT
preFLT
Preg
PRT
PTN-OSF1
PWB
Q
Quad
R
R
R1
R2
RAD51
RAW2647cells
RBCs
RCCS
RDSA
Rep
RIN
RL
RLT
Rminus
RNA
RNAlat
Rnor
Rotation
Rplus
RPoM
RR
RR-4_BMP_F#
RR-4_NSB#-L
RR-4_ShF#-W
RR-4_ShG#-L
RR-4_ShV#-W
RR-4_TPO_G#
RTN
RWV
RWV-H
RWV-V
S
S#
S-UHRR
S288C
Saur
scAem
scBem
Scer
scWim
SDR
SDR-TF
SecondSet
Sham
sham-infd
shamIR
shamSx
Si
SIEV
SKF
SKN
sl
sl-pool
SL1344
SLS
SM
SMK
Smut
soFLT
soGC
SP
SPL
ss-tissues
sShoots
Styp
suG
suppO2
Sx
sym
T
T
TA
Tcells
TES
TGFB
TGFB-Het
TGFP-ODsRed
ThirdSet
TIB
tissues
TK6cells
TKSC
TLCs
TMS
TNG
TNR
TRHLLC
TRIB
Trp53N-MG
Trp53N-MGT
TT
tumor
U
U937
UAMS-1
UdCC
uG
ug-mL
UHRR
um
UMRR
uni
uninfd
URR
uvr8
V
V
V#
VAC
VIV
VL
W
w1118
WAT
WB
WBCs
WCar
wk
WN1106
WN624
wo
Ws
Ws-0
Ws-2
WT
X
X-ray
Y
y
yo
YR
Z
Zone-I
Zone-II