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Sample inventory
In general, samples that were transported at room temperature were stored in the -20ºC freezer, while those transported
in the dry shipper were either left in the dry shipper or stored at -70ºC.
Those highlighted in yellow are at NMMBA (Taiwan) for long-term storage.
Those highlighted in purple are in -20ºC freezer at 842 N. Capital Ave., Indy (USA)
Those highlighted in green were sent to Nikki Traylor-Knowles in October, 2016.
Location 1
Location 2
buffer
notes
Australs-Cooks, April-May 2013 (extractions were performed at ULL in Oct.-Dec., 2013 and Jan., 2014)
N=122, of which ~90 were analyzed fully (gene expression [NMMBA] and genotyping [NMMBA and ULL, 88 in 1st Platax manuscript])
3 boxes in Indiana, 1.5 boxes of DNA @ NMMBA, 1 box of tissues to send to Nikki
Tissues (molecular)a
-20ºC (1 box @ NMMBA; n=25)
RNALater
All homogenized
92 with Nikki (homogenized in RNALater)
Tissues (microscopy)b
NMMBA office
n=28
RNA (concentrated)
-20ºC (1 box @ Indy)
Several @ NMMBA
DEPC-H20
No cDNAs remain (used all)
RNA (diluted)
-20ºC (1 box @ Indy)
Sufficient for one additional RT rxn
20 ng/ul
DNA (concentrated)
-20ºC (1 box) @ NMMBA
Axygen eluent
No diluted DNAs remain(w/Hollie)
protein
-20ºC 1 box @ Indy)
1.4 ml acetone
Purify at later date
Fiji, June 2013 (extractions were performed at ULL in March-April, 2014)
N=153, of which 90 were analyzed for gene expression, and 96 have been genotyped as of 9-7-16.
Tissues (molecular)c
-20ºC (2 boxes @ NMMBA, 80-90 remain)
RNALater
All but one were homogenized
73 in RNALater (all homogenized) with Nikki
Tissues (microscopy)b
NMMBA office
n=33
RNA (concentrated)
-20ºC (1.5 boxes @ Indy)
DEPC-H20
RNA (diluted)
-20ºC (1.5 boxes @ Indy)
DEPC-H20
20 ng/ul
DNA (concentrated)
-20ºC (3 boxes) @ NMMBA
Axygen eluent
No cDNAs remain (used all)
DNA (diluted)
-20ºC (3 boxes) @
Axygen eluent +
10 ng/ul
NMMBA
DEPC-H20
protein
-20ºC (1 box) @ Indy
-20ºC (1 box) @ NMMBA 1.4 ml acetone
Purify at later date
Tonga, September 2013 (extractions were performed at ULL in Fall-Winter 2014-2015)
N=115, of which 90 were analyzed (45 from Ha’apai and 45 from Va’vau) for gene expression/genotyping
Tissues (molecular)c,d
-20ºC (2 boxes @
Give to Nikki or Luisa in
RNALater, plant
Extracted @ ULL in Oct. Dec.,
NMMBA)
early 2017
lysis buffer
2014 and Jan. 2015
Tissues (microscopy)b
NMMBA office
n=31
RNA (concentrated)
-20ºC (2-3 boxes)
DEPC-H20
Concentrated and diluted are in
n=90
same box
DNA (concentrated)
-20ºC (2 boxes) @
Axygen eluent
Concentrated and diluted are in
n=90
NMMBA
same box
DNA (diluted)
-20ºC (2 boxes) @
Axygen eluent+
No cDNAs remain
NMMBA
milliQ water
Protein (precipitated)
-20ºC (1 box)
Acetone or
Purify at later date
isopropanol
New Caledonia, November 2013 (perform extractions in mid-2015 at NMMBA) N=139, 120 analyzed in September, 2015.
Tissues (molecular)c
-20ºC (2 boxes)
-20ºC (1 box, transferred RNALater
Extracted @ NMMBA in July 2015
Only process nonto -70C in Feb. 2015)
(homogenized and
homogenized samples
non-homogenized
RNA (concentrated,
-20ºC NMMBA (2 boxes)
DEPC-H20 (30 ul)
n=120)
RNA (diluted, n=120)
-20ºC NMMBA (2 boxes)
DEPC-H20 (21 ul)
DNA (concentrated,
-20ºC NMMBA (2 boxes)
“Eluent” (50 ul)
n=120)
DNA (diluted, n=120)
-20ºC NMMBA (2 boxes)
DEPC-H20 (50 ul)
cDNA (5-10)
-20ºC NMMBA (1 box)
DEPC-H20 (80 ul)
Used all for most samples
Protein (n=130-140)
-20ºC NMMBA (1 main box, rest over several boxes) Precipitated in acetone
Tissues (microscopy)b
NMMBA office
paraffin
n=28+6 w/ missing labels
Solomon Islands, November 2014 (performed extractions in 2016) all samples except for several diluted DNAs are at NMMBA
Pocillopora sp. (mostly P. acuta) and N=200 Seriatopora sp. (mix of SH and SC, gave to Noodle in early Feb. 2015)
Tissues (molecular)
-20ºC freezer in RBII
Transported all samples to Taiwan
N=126
in Feb. 2015
Tissues (microscopy) n=36
NMMBA office
paraffin
RNA (concentrated,
-20ºC freezer in RBII
n=120)
(across 2 boxes)
RNA (diluted, n=120)
-20ºC freezer in RBII (across 2 boxes)
DNA (concentrated,
-20ºC freezer in RBII (across two boxes)
n=138)
DNA (diluted, n=100)
Indy (10-20 samples)
Mailed remainder ~(100)
Used all cDNA for assays
to Nikki in Sept. 2016
(Solaris+8 genes)
Protein (n=130-140) -20ºC freezer in RBII (across two boxes)
Palau, January 2015, 185 samples across 150 unique colonies, five night dives, may have been at room temperature for 2-3 days
Tissues (molecular, n=185) -20ºC freezer in RBII
RNALater (none were homogenized)
TRIzol (n=113) Only process TRIzol samples
Tissues (microscopy, n=35) NMMBA office
PBS
Embedded by BB
RNA (concentrated, n=160) 2 boxes in -20ºC freezer
DEPC-H20 (30 ul)
in RBII
RNA (diluted, n=160)
2 boxes in -20ºC freezer
DEPC-H20 (11 ul)
in RBII
cDNA (n=150)
Indy
DNA (concentrated, n=160) 2 boxes -20ºC freezer in
Protech kit eluent
RBII
(50 ul)
DNA (diluted, n=160)
Indy
DEPC-H20 (50 ul)
Protein (n=160)
-20ºC freezer in RBII
acetone (~1.5 ml)
Chagos, March-April 2015 (two missions): 166 P. acuta/damicornis samples (140 in TRIzol to process), 174 Seriatopora spp. samples, and
312 other Pocillopora sp. samples for Joao
Tissues (molecular)
2 boxes (n=166) NMMBA
RNALater (1.5-1.7
Took to Taiwan in May 2015 at RT
-80C
ml/sample)
Tissues (molecular)
2 boxes (n=140)
Gave to Pi in on 9-20-16
TRIzol (650-1,500
Took to Taiwan in May 2015 at RT
2016 (-20C)
ul/sample)
1.5 ml PBS, EDTA,
or FSW
Seriatopora spp.
3 boxes (n=175)
1.5 ml DESS
Seriatopora spp.
1 box (n=30) in -20C @
Gave to Pi in October
1.5 ml TRIzol
NMMBA
2016
1.7 ml RNALater
Joao samples
3 boxes (n=312,
Taken by Andy
1.5 ml DESS or
156/cruise)
80% ethanol
Maldives, January, 2016 (two weeks): 87 Pocillopora spp. and 79 Acropora spp. samples
Tissues (molecular)
0.5 box
-20ºC @ NMMBA
RNALater
First ~30 samples only
Give to Luisa in Oct.
2016
Tissues (molecular)
2 boxes
Gave to Pi on 9-20-16
TRIzol
All 166 samples
(n=166)
Tissues (molecular)
2 boxes (post-bleaching) -20ºC @ Indy
RNALater
N=?
Dongsha, March, 2016: 28 P. acuta/damicornis samples in TRIzol only
1 box in Pi’s -20ºC
a All samples were transported from ship to ULL at room temperature.
b Samples were fixed, washed, decalcified, washed w/ PBS, & transported from the ship to ULL (& later to Taiwan) in PBS.
c Some samples were transported from the ship to ULL via dry shipper (-150ºC).
d Some samples are stored in GeneMark plant lysis buffer (non-homogenized).
Tissues (microscopy)
NMMBA office
Australs-Cooks
+1 box with concentrated RNA
+1 box with diluted RNAs (both concentrated and diluted)
+1 box with proteins precipitated in acetone (some samples in other boxes)
=3 total in Indy freezer + 1.5 boxes of RNA and DNA (concentrated only) and 1 box of remaining tissues @ NMMBA
Fiji
1.5 boxes with RNA (concentrated and diluted; some RNAs are in Taiwan)
1 box with proteins precipitated in acetone
= 2.5 total in Indy+ 6.5 boxes @ NMMBA (see list below)
Tonga:
+2 boxes with RNA (concentrated and diluted)
+1 box with proteins
= 2.5 total in Indy + 4 boxes of DNA @ NMMBA
Solomon Islands
10-20 DNAs in box with Maldives samples.
Palau
2 boxes with cDNAs
+2 boxes with diluted DNAs +concentrated and diluted RNAs, precipitated proteins, concentrated DNAs, and all
tissues are at NMMBA
Additional boxes at Indy -20C freezer
1. primer box 1 includes DNase and some other reagents
2. primer box 2
Total boxes in Indiana:
3 A/C boxes (including remaining reagents)+ 2.5 Fiji boxes+2.5 Tonga boxes+2 Maldives boxes (post-bleaching)+2
primers boxes =12 boxes in freezer
posi
tion
1
2
3
4
NMMBA samples. Green=pack up and bring to US to give to Nikki.
-20C rack 1: reagents and NSF -20C rack 2: NSF rack 2 and LOF rack -20C rack 3: LOF rack 2:
samples
1: A/C and Fiji
Fiji, Tonga, and NC
PCR reagents & primers
NO SLOT
NO SLOT
PCR reagents (Hsiao)
Misc. NSF DNAs and cDNA
NO SLOT
PCR/cloning reagents (Hsiao)
Misc. NSF samples
Fiji DNA
Lab reagents
PDLTTE DNA, cDNA, and TEM
Fiji DNA (diluted)
-20C rack 4: LOF rack 4: New
Caledonia and Dongsha
NO SLOT
NC tissues
NC RNAs (concentrated) 1-62
NC RNAs (concentrated) 63-104
5
SHVTS primers
6
Symbiodinium primers
7
PD and other primers
8
Cardboard primer box (mine
and Hsiao’s)
9
Hsiao’s primers
10
PDpCO2 DNAs
11
SHVTS tissues and DNAs
capsules
PDSTTE#2 cDNA, DNA, and Pi’s
mesocosm samples
Misc. NSF samples and Pi’s pCO2
mesocosm samples: tissues in TRIzol
Pi’s pCO2 mesocosm samples: tissues
in TRIzol
Australs/Cooks DNAs
Fiji DNAs and tissues
-20C rack 5: LOF rack 5: Solomon Islands
1
2
3
4
5
6
7
8
9
10
Solomon Islands tissues in RNALater+proteins
Solomon Islands tissues in RNALater
Solomon Islands tissues in RNALater and PLB
Solomon Islands RNAs
Solomon Islands RNAs (diluted)
Solomon Islands diluted RNAs and cDNAs
Solomon Islands DNAs
Solomon Islands DNAs (diluted)
Solomon Islands DNAs (diluted)
Solomon Islands proteins
Fiji DNA (diluted) w/
some Australs-Cooks
DNA (~10 samples)
Fiji: proteins and tissues
and proteins
NC RNAs (diluted) 1-75
Tonga tissues
NC diluted RNAs, DNA, and
cDNAs (n=10 only)
NC DNAs (concentrated) 1-76
Tonga tissues + DNAs
NC DNAs (concentrated) 77-104D
Tonga DNAs 1-49
(concentrated & diluted)
Tonga DNAs 50-98
(concentrated & diluted)
N NC tissues in RNALater+
some proteins
-20C rack 6: Solomon Islands, Palau,
Chagos, and Maldives
Solomon Islands RNAs and proteins
Palau tissues (TRIzol and RNALater) #1
Palau tissues (TRIzol and RNALater) #2
Palau RNAs #1
Palau RNAs #2
Palau DNAs #1
Palau DNAs #2
Palau proteins #1
Palau proteins #2
Palau mixed
NC DNAs diluted: 1-81
NC proteins
Dongsha samples: 1-28
-20C rack 7:
Palau cDNA
Chagos 1-PD in RNALater and TRIzol
Chagos 2-PD in TRIzol
Chagos 3-Seriatopora in TRIzol
Ruth’s samples in guanidinium
Maldives tissues #1
Maldives tissues #2
HTT primers and reagents
Rack #8 in office (can hold 10 more boxes). Will generate 8-10 boxes for 166 Chagos samples
Maldives tissues #3
LOF sample processing: Green = completed. Yellow=in progress. Red=2016.
Cruise (#)
Dates
Sample Extractions GCPb Symbiodinium Host
Gene expression
a
size
genotype
genotype
Australs/
Apr.-May
123/28 100/123
60/10 60/100
89/100
Solarisd+6 Sym gene
Cooks (1)
2013
0
0 host genesc
Fiji (2)
June 2013 153/33 91/153
90/91 90/91
94/153
Solaris+ 4 Sym
genes+ 4 host genes
Tonga (3)
Sept. 2013 115/31 90/115
90/90 90/90
~112/115 Solaris+4 Sym genes+
4 host genes
New (4)
Nov. 2013 139/28 120/139
120/ 120/120
~100
Solaris+4 Sym genes+
Caledonia
125
4 host genes
GBR (5)
Sept. 2014 No sampling
Solomon
Oct.-Nov.
125/35 138/145
120/ (n=120)
111
Solaris+4 Sym
Islands (6) 2014
120
genes+4 host genes
Palau (7)
Jan. 2015
185/35
150/185
150/
150
n=150/150
Fall 2016
Solaris+4 Sym genes
+ 4 host genes (target
Notes/other/to-do
1. Image analysis
1. Write manuscript
1. Morphology differences
2. Species difference
1. Light-dark differences
within a sample
1. Analyze data
1. Light-dark differences
within a sample
2. Healthy-bleached within
sample differences
1. Light-dark differences
within a sample
new genes)
Chagos
(8-9)
Chagos
(8-9)
Maldivese
(10)
Dongshae
(11)
TOTAL
Mar.-May
2015
Mar.-May
2015
166/70 Poc. Sp. Extract
from 150 (TRIzol only)
30 Seriatopora sp. in
TRIzol. Extract all
winter 2017
winter 2017
winter 2017
winter 2017
2. Healthy-bleached within
sample differences
1. Naturally bleached
transcriptome/proteome
1. healthy vs. bleached
proteomics
2. Noodle has 174 samples
1. Pre-, during and postbleaching comparison
2. Pre- and post-bleaching
87 Pocillopora spp.
Spring 2017
Spring 2017
79 Acropora spp.
Mar. 2016 28 Pocillopora
Late 2017
Late 2017
damicornis/acuta
~1,000 Pocillopora sp. (1,034)
620 dives
1.
~575 Seriatopora sp. (574-600)
aThe first and second values represent the total for molecular and histological analyses, respectively.
bproxy for Symbiodinium density.
cdid not assess due to having mix of different species.
dexogenous control
enot LOF samples.
Jan. 2016
LOF samples. Those in yellow are in the US (Indianapolis), while those in purple are in Taiwan. Samples highlighted in green are
with Nikki in Miami. The RNAs are either fully concentrated (typically around 100 ng/ul) or diluted to 20 ng/ul. The DNAs are either
fully concentrated (typically around 150 ng/ul) or diluted to 10 ng/ul. The cDNAs are all the equivalent of 200 ng RNA (i.e., 200 ng
RNA was used in the RT rxn).
Location
Tissues (buffer)
Tissues (form)
RNA cDNA DNA protein
Paraffin
TEM/SEM
blocks
Typically TRIzol® or frozen in
Every form imaginable
✔
Taiwan
✔
✔
✔
✔
✔
FSW (n=~150 over various
(nubbins, slurry, small
buffers)
projects)
fragments, etc.)
RNALater (n=61)
Homogenized only
✔✔a
✔b
✔ (precipitated ✔
Austral Islands
)
a
RNALater
Homogenized only
✔✔
✔ (precipitated ✔
Cook Islands
✔
✔
(n=61)
)
(precipitated
✔
(precipitated
✔
(precipitated
✔
(precipitated
✔
(precipitated
✔
5)
Late 2016
✔
60)
2017
0
Fiji
RNALater (n=153)
Homogenized only
✔
✔
✔
Tonga
RNALater (n=115)
✔
✔
✔
New Caledonia
RNALater (n=150)
✔
✔
✔
Solomon Islandsc
RNALater (n=125)
Homogenized &
unhomogenized
Homogenized &
unhomogenized
unhomogenized
✔
✔
✔✔✔
Palau
RNALater (n=150)
TRIzol (n=113)
RNALater (n=165)
TRIzol (n=165)
RNALater (n=30)
TRIzol (n=166)
RNALater (n=?)
TRIzol only (n=28)
unhomogenized
✔
✔
✔
unhomogenized
unhomogenized
Chagos (i.e.,
BIOT)
Maldives (not
LOF samples)
✔
)
✔
)
✔
)
✔
)
✔
)
Dongsha (not LOF
unhomogenized
Not suitable for skeleton analysis
0
samples)
Total ~1,200 (though many, if not the majority, are NOT the alpha genotype (i.e., the archetypal P. damicornis)
a
Would need to re-synthesize cDNA. bSome diluted DNAs are Hollie. cAlso have Seriatopora hystrix from this cruise onwards (~100
colonies/cruise).