Table 1 Open in new tab Summary of...

	MED4	MIT9313	Reference
Ecotype adapted to	High light	Low light	Moore et al., 1995
Hfq	No	Yes	Axmann et al., 2005
Genome size	1.66 Mbp	2.41 Mbp	Rocap et al., 2003
Annotated protein-coding genes	1974	2.894	Kettler et al., 2007
	454 sequencing	Solexa sequencing	454 sequencing	Solexa sequencing
Total number of mapped reads	61 633	5 750 991	113 994	4 663 103
Number of reads w/o ribosome	40 739	5 425 895	59 761	3 712 862
Total number of TSS^a	1643	3459	3402	7410
gTSS	608	1059	801	1284
iTSS	423	658	928	2256
aTSS	520	1566	1372	3231
nTSS	92	176	300	639
aTSS with most reads	asPMED4_06291 (clpB, 52 reads)	asPMED4_04671 (cons. hyp., 21 506 reads)	asP9313_16021 (priA, 184 reads)	asP9313_06941 (recG, 3542 reads)	This work
gTSS with most reads	PMED4_11782 (cons. hyp., 482 reads)	PMED4_16461 (groES, 93 670 reads)	P9313_14931 (psbD, 263 reads)	P9313_20011 (smc, 124 649 reads)
nTSS with most reads	Yfr11 (1700 reads)	Yfr16 (1 184 303 reads)	Yfr103 (413 reads)	Yfr2-5 (48 227 reads)
Filter criteria for TSS mapping	⩾2 reads, score⩾2.0	⩾26 reads, score⩾2.0	⩾2 reads, score⩾2.0	⩾24 reads, score⩾2.0

MED4

MIT9313

Reference

Ecotype adapted to

High light

Low light

Moore et al., 1995

Hfq

Yes

Axmann et al., 2005

Genome size

1.66 Mbp

2.41 Mbp

Rocap et al., 2003

Annotated protein-coding genes

1974

2.894

Kettler et al., 2007

454 sequencing

Solexa sequencing

454 sequencing

Solexa sequencing

Total number of mapped reads

61 633

5 750 991

113 994

4 663 103

Number of reads w/o ribosome

40 739

5 425 895

59 761

3 712 862

Total number of TSS^a

1643

3459

3402

7410

gTSS

608

1059

801

1284

iTSS

423

658

928

2256

aTSS

520

1566

1372

3231

nTSS

176

300

639

aTSS with most reads

asPMED4_06291 (clpB, 52 reads)

asPMED4_04671 (cons. hyp., 21 506 reads)

asP9313_16021 (priA, 184 reads)

asP9313_06941 (recG, 3542 reads)

This work

gTSS with most reads

PMED4_11782 (cons. hyp., 482 reads)

PMED4_16461 (groES, 93 670 reads)

P9313_14931 (psbD, 263 reads)

P9313_20011 (smc, 124 649 reads)

nTSS with most reads

Yfr11 (1700 reads)

Yfr16 (1 184 303 reads)

Yfr103 (413 reads)

Yfr2-5 (48 227 reads)

Filter criteria for TSS mapping

⩾2 reads, score⩾2.0

⩾26 reads, score⩾2.0

⩾2 reads, score⩾2.0

⩾24 reads, score⩾2.0

	MED4	MIT9313	Reference
Ecotype adapted to	High light	Low light	Moore et al., 1995
Hfq	No	Yes	Axmann et al., 2005
Genome size	1.66 Mbp	2.41 Mbp	Rocap et al., 2003
Annotated protein-coding genes	1974	2.894	Kettler et al., 2007
	454 sequencing	Solexa sequencing	454 sequencing	Solexa sequencing
Total number of mapped reads	61 633	5 750 991	113 994	4 663 103
Number of reads w/o ribosome	40 739	5 425 895	59 761	3 712 862
Total number of TSS^a	1643	3459	3402	7410
gTSS	608	1059	801	1284
iTSS	423	658	928	2256
aTSS	520	1566	1372	3231
nTSS	92	176	300	639
aTSS with most reads	asPMED4_06291 (clpB, 52 reads)	asPMED4_04671 (cons. hyp., 21 506 reads)	asP9313_16021 (priA, 184 reads)	asP9313_06941 (recG, 3542 reads)	This work
gTSS with most reads	PMED4_11782 (cons. hyp., 482 reads)	PMED4_16461 (groES, 93 670 reads)	P9313_14931 (psbD, 263 reads)	P9313_20011 (smc, 124 649 reads)
nTSS with most reads	Yfr11 (1700 reads)	Yfr16 (1 184 303 reads)	Yfr103 (413 reads)	Yfr2-5 (48 227 reads)
Filter criteria for TSS mapping	⩾2 reads, score⩾2.0	⩾26 reads, score⩾2.0	⩾2 reads, score⩾2.0	⩾24 reads, score⩾2.0

Table 1

Open in new tab

Summary of genome and transcriptome information. Sequencing numbers are given for primary libraries only

	MED4		MIT9313		Reference
Ecotype adapted to	High light		Low light		Moore et al., 1995
Hfq	No		Yes		Axmann et al., 2005
Genome size	1.66 Mbp		2.41 Mbp		Rocap et al., 2003
Annotated protein-coding genes	1974		2.894		Kettler et al., 2007
	454 sequencing	Solexa sequencing	454 sequencing	Solexa sequencing
Total number of mapped reads	61 633	5 750 991	113 994	4 663 103
Number of reads w/o ribosome	40 739	5 425 895	59 761	3 712 862
Total number of TSS^a	1643	3459	3402	7410
gTSS	608	1059	801	1284
iTSS	423	658	928	2256
aTSS	520	1566	1372	3231
nTSS	92	176	300	639
aTSS with most reads	asPMED4_06291 (clpB, 52 reads)	asPMED4_04671 (cons. hyp., 21 506 reads)	asP9313_16021 (priA, 184 reads)	asP9313_06941 (recG, 3542 reads)	This work
gTSS with most reads	PMED4_11782 (cons. hyp., 482 reads)	PMED4_16461 (groES, 93 670 reads)	P9313_14931 (psbD, 263 reads)	P9313_20011 (smc, 124 649 reads)
nTSS with most reads	Yfr11 (1700 reads)	Yfr16 (1 184 303 reads)	Yfr103 (413 reads)	Yfr2-5 (48 227 reads)
Filter criteria for TSS mapping	⩾2 reads, score⩾2.0	⩾26 reads, score⩾2.0	⩾2 reads, score⩾2.0	⩾24 reads, score⩾2.0

	MED4		MIT9313		Reference
Ecotype adapted to	High light		Low light		Moore et al., 1995
Hfq	No		Yes		Axmann et al., 2005
Genome size	1.66 Mbp		2.41 Mbp		Rocap et al., 2003
Annotated protein-coding genes	1974		2.894		Kettler et al., 2007
	454 sequencing	Solexa sequencing	454 sequencing	Solexa sequencing
Total number of mapped reads	61 633	5 750 991	113 994	4 663 103
Number of reads w/o ribosome	40 739	5 425 895	59 761	3 712 862
Total number of TSS^a	1643	3459	3402	7410
gTSS	608	1059	801	1284
iTSS	423	658	928	2256
aTSS	520	1566	1372	3231
nTSS	92	176	300	639
aTSS with most reads	asPMED4_06291 (clpB, 52 reads)	asPMED4_04671 (cons. hyp., 21 506 reads)	asP9313_16021 (priA, 184 reads)	asP9313_06941 (recG, 3542 reads)	This work
gTSS with most reads	PMED4_11782 (cons. hyp., 482 reads)	PMED4_16461 (groES, 93 670 reads)	P9313_14931 (psbD, 263 reads)	P9313_20011 (smc, 124 649 reads)
nTSS with most reads	Yfr11 (1700 reads)	Yfr16 (1 184 303 reads)	Yfr103 (413 reads)	Yfr2-5 (48 227 reads)
Filter criteria for TSS mapping	⩾2 reads, score⩾2.0	⩾26 reads, score⩾2.0	⩾2 reads, score⩾2.0	⩾24 reads, score⩾2.0

Abbreviation: w/o, without.

Total number of TSS after clustering of neighboring TSS that start ±10 nt of each other or have a similar ±3 nt −10 element (as described above) and removal of potential processing sites (primary coverage is lower than secondary coverage).

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