Skip to end of metadata
Go to start of metadata

Normalized cDNA libraries for Daphnia pulex

Treated Daphnia pulex (the Chosen One) were obtained from Jacqueline Lopez (Indiana University), Joe Shaw (Dartmouth College), Darren Bauer (University of New Hampshire), Rebecca Klaper (Great Lakes WATER Institute) and Tom Little (University of Edinburgh). RNA was isolated in accordance with the Daphnia RNA protocol . After inspection with the Agilent 2100 Bioanalyzer, RNA was used to construct normalized cDNA libraries using the Trimmer-Direct kit from Evrogen.

Library

Tube I.D.

Stage

Date Completed

Titer (cfu/mL)

1

Juvenile Female 2

4 day old female

2/07/06

5.85x10^8

2

Adult Female 2

10 day old female

2/06/06

7.2x10^7

3

Male 1

10 day old male

2/06/06

5.6x10^8

4

Dart 4

Nickel - 200 ug Ni/L as nickel chloride

4/10/06

2.08x10^8

5

Dart 5

Copper - 5 ug Cu/L as copper sulfate

4/10/06

1.64x10^8

6

Dart 6

pH 6 - combined 1st and 2nd generation

4/10/06

1.81x10^8

7

Dart 8

High salinity - 750 mg/L of chloride as sodium chloride

4/10/06

2.48x10^8

8

Dart 10

Fullerene nanoparticles - 3 days old females

4/4/06

6.2x10^8

9

Dart 9

Bacteria infection

5/11/06

1.4x10^8

10

Dart 2

Mixed metals (high) - 20 ug Cd/L; 200 ug Zn/L; 1348 ug As/L

5/2/06

4.8x10^8

11

Dart 1

Mixed metals (low) - 1 ug Cd/L; 50 ug Zn/L; 500 ug As/L

5/2/06

7.6x10^8

12

Dart 3

Monomethylarsenic III - 100 ug As/L as diiodo-MMAIII

5/11/06

4.2x10^7

13

Dart 11

Titanium Dioxide nanoparticles - 5 days old females

5/10/06

4.5x10^8

14

Dart 12

Microcystis

5/10/06

6.8x10^8

15

Dart 13

Calcium starvation - 1 mg/L of Ca; second generation harvested

5/10/06

7x10^8

Download complete library descriptions

Details on normalized cDNA library construction

PCR based analysis of cDNA inserts

Using the primers above, the 96 well QC plates were PCR amplified and run out on 1.5% TAE gels. The results can be found here

Initial quality control sequencing results

For each library, one 96-well plate was sequenced from cDNA archived in a 384-well plate. The sequencing protocol can be found here. The resulting sequences were processed using TIGR Lucy and CAP3 using the CGB EST Pipeline Analysis Pipeline. The EST sequences were also compared against the current Daphniagenome sequence to ascertain the probablity of chimeric sequences. We are confident that there are no such sequences in these libraries. The data for the QC sequencing can be found here.

Summary of the CGB quality control sequence data

Library

Tube ID

Starting Sequences

Sequences Passed by TIGR Lucy

Excluded by Sequence Trimming

Sequences input into CAP3

Contigs

Singlets

Redundancy

Gene Discovery Rate

1

Juvenile Female

96

89

14

75

0

75

0%

100%

2

Adult Female

96

85

1

84

1

82

2.38%

97.62%

3

Adult Male

96

87

11

76

0

76

0%

100%

11

Dart 1

96

93

1

92

0

92

0%

100%

10

Dart 2

96

72

1

71

0

71

0%

100%

12

Dart 3

96

87

3

84

0

84

0%

100%

4

Dart 4

96

89

1

88

0

88

0%

100%

5

Dart 5

96

88

4

84

0

84

0%

100%

6

Dart 6

96

90

1

89

0

89

0%

100%

7

Dart 8

96

86

3

83

1

81

2.38%

97.62%

9

Dart 9

96

80

0

80

0

80

0%

100%

8

Dart 10

96

81

5

76

0

76

0

100%

13

Dart 11

96

79

7

72

0

72

0%

100%

14

Dart 12

96

92

1

91

0

91

0%

100%

15

Dart 13

96

82

8

74

0

74

0%

100%

JGI quality control sequencing of a 384-well plate from all 15 libraries

Download complete report

Synonym table

  • CBIA = Library 1 (Juvenile female)
  • CBIB = Library 2 (Adult female)
  • CBIC = Library 3 (Adult male)
  • CBNN = Library 4 (Nickel toxicity)
  • CBNO = Library 5 (Copper toxicity)
  • CBNP = Library 6 (Acid stress pH 6.0)
  • CBNS = Library 7 (Salinity stress)
  • CBNT = Library 8 (Fullerene nanoparticles)
  • CBTO = Library 9 (Bacteria infection)
  • CBTP = Library 10 (Mixed metals (high))
  • CBTS = Library 11 (Mixed metals (low))
  • CBTT = Library 12 (Monomethylarsenic III)
  • CBTU = Library 13 (Titanium Dioxide nanoparticles)
  • CBTW = Library 14 (Microcystis)
  • CBTX = Library 15 (Calcium starvation)
Cluster                                     Total                              ESTs in
Revision Description                        ESTs    Clones  Libraries Clusters Clusters Singlets
======== ================================== ======= ======= ========= ======== ======== ========
725      Daphnia pulex The Chosen One QC    8323    4488    15        3372     7777     546
         batch v1.1.1

Library ESTs   Singlets Clusters
======= ====== ======== ========
CBIA    211    28       89
CBIB    582    42       272
CBIC    496    28       228
CBNN    645    37       303
CBNO    579    69       253
CBNP    653    50       304
CBNS    647    21       311
CBNT    549    37       256
CBTO    598    18       292
CBTP    465    40       214
CBTS    635    45       296
CBTT    583    49       269
CBTU    541    18       259
CBTW    605    36       278
CBTX    534    28       252


NOTE: For the following analysis, 'clusters' includes 'singlets', which are just clusters of 1.

                                                             ESTs         % Group ESTs % Total ESTs Clones       Exclusive
                                   % Total         Exclusive In Exclusive In Exclusive In Exclusive In Exclusive Clusters
Group                      ESTs    ESTs    Clones  Clusters  Clusters     Clusters     Clusters     Clusters     with >1 Clone
========================== ======= ======= ======= ========= ============ ============ ============ ============ =============
CBIA                       211     2.54    121     101       180          85.31        2.16         104          2
CBIB                       582     6.99    318     251       465          79.90        5.59         254          3
CBIC                       496     5.96    263     218       414          83.47        4.97         221          3
CBNN                       645     7.75    345     282       533          82.64        6.40         286          4
CBNO                       579     6.96    327     264       466          80.48        5.60         268          4
CBNP                       653     7.85    356     281       515          78.87        6.19         283          2
CBNS                       647     7.77    336     257       501          77.43        6.02         261          4
CBNT                       549     6.60    298     227       419          76.32        5.03         228          1
CBTO                       598     7.18    314     254       490          81.94        5.89         254
CBTP                       465     5.59    256     205       373          80.22        4.48         207          2
CBTS                       635     7.63    343     256       469          73.86        5.63         257          1
CBTT                       583     7.00    320     255       464          79.59        5.57         257          2
CBTU                       541     6.50    282     211       412          76.16        4.95         215          4
CBTW                       605     7.27    322     230       432          71.40        5.19         234          4
CBTX                       534     6.42    287     210       399          74.72        4.79         214          4

                           Exclusive Exclusive    Inclusive Inclusive
                           Union     Intersection Union     Intersection
Group                      Clusters  Clusters     Clusters  Clusters
========================== ========= ============ ========= ============
CBIA                       101       101          16        16
CBIB                       251       251          63        63
CBIC                       218       218          38        38
CBNN                       282       282          58        58
CBNO                       264       264          58        58
CBNP                       281       281          73        73
CBNS                       257       257          75        75
CBNT                       227       227          66        66
CBTO                       254       254          56        56
CBTP                       205       205          49        49
CBTS                       256       256          85        85
CBTT                       255       255          63        63
CBTU                       211       211          66        66
CBTW                       230       230          84        84
CBTX                       210       210          70        70


Definitions:
- Exclusive: containing only libraries in the group.
- Inclusive: containing one or more libraries in the group, as well as other libraries.

- Exclusive Union: only libraries in the group, with at least 1 EST from at least 1 of the libraries.
- Exclusive Intersection: only libraries in the group, with at least 1 EST from each of the libraries.

- Inclusive Union: includes other libraries, with at least 1 EST from at least 1 of the libraries.
- Inclusive Intersection: includes other libraries, with at least 1 EST from each library.
  • No labels