1-day old seedling

S.H - Seedling hypocotyl

Hypocotyl of one-day-old seedling from place of the attachment of cotyledons to the beginning of root.

S.M - Seedling meristem

Seedling shoot apical meristem with adjacent tissues.

S.C - Seedling cotyledons

Cotyledons of one-day-old seedling, collected with petioles.

S.R - Seedling root

Root of one-day old seedling. Immediately before collection seedlings were gently pulled out ofsoil and washed under fresh water.

Leaf

All leaf samples were taken from the third leaf, if other not indicated. Samples were collected at 5 stages: 7 days after germination (young, ~ 3mm in length), 9 days after germination (intermediate 1, ~ 5 mm in length), 12 days after germination (intermediate 2, ~ 10 mm in length), at the moment of anthesis of the first flower (mature leaf) and at the stage of maturation of seeds in first siliques (senescent leaf).

	L.PET.y - Petiole of the young leaf Petiole of the third leaf. Sample was collected at 7th day after germination (3 mm leaf).
	L.LAM.y - Leaf blade of the young leaf Leaf blade of the third leaf. Sample was collected at 7th day after germination (3 mm leaf).
	L.PET.i1 - Petiole, intermediate 1 Petiole of the third leaf. Sample was collected at 9th day after germination (5 mm leaf).
	L.LAM.i1 - Leaf blade, intermediate 1 Leaf blade of the third leaf. Sample was harvested at 9th day after germination (5 mm leaf).
	L.PET.i2 - Petiole, intermediate 2 Petiole of third leaf. Sample was collected at 12th day after germination (10 mm leaf).
	L.VN.i2, Leaf vein, intermediate 2 Midrib of the third leaf. Sample was collected at 12th day after germination (10 mm leaf).
	L.LAM.i2 - Leaf blade, intermediate 2 Parts of the leaf blade without veins. Sample was collected at 12th day after germination (10 mm leaf).
	L.lg - mature leaf Whole third leaf. Sample was collected at the moment of anthesis of the first flower.
	L.PET.lg - Petiole of the mature leaf Petiole of the third leaf. Sample was collected at the moment of anthesis of the first flower.
	L.VN.lg - Vein of the mature leaf Midrib of the third leaf. Sample was collected at the moment of anthesis of the first flower.
	L.LAM.lg - Leaf blade of the mature leaf Parts of the leaf blade without veins. Sample was collected at the moment of anthesis of the first flower.

L.PET.sn - Petiole of the senescent leaf

Petiole of the third leaf. Sample was collected when first silique was completely mature and nearly opened.

L.VN.sn - Vein of the senescent leaf

Midrib of the third leaf. Sample was collected when first silique was completely mature and nearly opened.

Flower (whole)

All samples of this series were collected at moment of the anthesis of the first flower.

	F1 - Flower 1 Whole flower 1 without pedicel.
	F2 - Flower 2 Whole flower 2 without pedicel.
	F3 - Flower 3 Whole flower 3 without pedicel.
	F4 - Flower 4 Whole flower 4 without pedicel.
	F5 - Flower 5 Whole flower 5 without pedicel.
	F6-8 - Flowers 6-8 Whole flowers 6, 7 and 8 without pedicel.
	F9-11 - Flowers 9-11 Whole flowers 9, 10 and 11 without pedicel.
	F12-14 - Flowers 12-14 Whole flowers 12, 13 and 14 without pedicel.
	F15-18 - Flowers 15-18 Whole flowers 15, 16, 17 and 18 without pedicel.
	F19+ - Flowers 19 and following Whole inflorescence apex from flower 19 to meristem.

Parts of the flower

	F.AN - Opened anthers Anthers of first flower; sample collected at the moment of the anthesis of the first flower.
	F.CA.ad - Carpels of the mature flower (before pollination Pistil of the third flower; sample collected at the moment of the anthesis of the first flower.
	F.AN.ad - Anthers of the mature flower (before opening). Anthers of the third flower; sample collected at the moment of the anthesis of the first flower.
	F.FM.ad - Stamen filaments of the mature flower Filaments of stamens of the third flower; sample collected at the moment of the anthesis of the first flower.
	F.PT.ad - Petals of the mature flower Petals of the third flower; sample collected at the moment of the anthesis of the first flower.
	F.SP.ad - Sepals of the mature flower Sepals of the third flower; sample collected at the moment of the anthesis of the first flower.
	F.CA.y - Carpels of the young flower Pistil of young flower (at stage 9 according to Smyth et al., 1990). Sample collected at the moment of the anthesis of the first flower.
	F.AN.y - Anthers of the young flower Anthers of young flower (at stage 9 according to Smyth et al., 1990). Sample collected at the moment of the anthesis of the first flower.
	F.SP.y - Sepals of the young flower Anthers of young flower (at stage 9 according to Smyth et al., 1990). Sample collected at the moment of the anthesis of the first flower.
	STI - Stigmatic tissue Stigmatic tissue from pistils of 6th and 7th flowers (before pollination). Sample collected at the moment of the abscission of the first flower.

POD.y6-7 - Carpel of 6th and 7th flowers

Pistils of 6th and 7th flowers (before pollination), ovules and stigma removed. Sample collected at the moment of the abscission of the first flower.

OV.y6-7 - Ovules from 6th and 7th flowers

Ovules from 6th and 7th flowers (before pollination). Sample collected at the moment of the abscission of the first flower.

Axes

All samples are collected at the moment of the anthesis of the first flower.

PED - Pedicel

Pedicel of the first flower.

Ax - Axis of the inflorescence

Axis of the inflorescence without flowers and pedicels.

IN - Internode

First elongated internode (from last rosette leaf to first cauline leaf).

Root

R.A - Root apex

Apex of the root, collected from plants at 7th day after germination.

R - Root

Root without apex, collected from plants at 7th day after germination.

Meristems

Detailed analysis of the expression profiles and morphology of the following three series (shoot apical meristem, transition to flowering and inflorescence meristem) is provided in recently published paper by Klepikova et al.

Shoot apical meristem

Scanning electron micrographs and photographs showing the developmental stages of the shoot apical meristem (SAM). The region that was collected as the meristem sample is false colored green in the SEM images. The rosette photographs provide a whole-plant view at the stages of collection.

	M1 - SAM at 7 days after germination
	M2 - SAM at 8 days after germination
	M3 - SAM at 9 days after germination

Transition to flowering

Scanning electron micrographs and photographs showing the meristem at the stage of transition to flowering. The region that was collected as the meristem sample is false colored green in the SEM images. The rosette photographs provide a whole-plant view at the stages of collection.

	M4 - meristem at 10 days after germination
	M5 - meristem at 11 days after germination
	M6 - meristem at 12 days after germination

Inflorescence meristem

Scanning electron micrographs and photographs showing the inflorescence meristem. The region that was collected as the meristem sample is false colored green in the SEM images. The rosette photographs provide a whole-plant view at the stages of collection.

	M7 - inflorescence meristem at 13 days after germination
	M8 - inflorescence meristem at 14 days after germination
	M9 - inflorescence meristem at 15 days after germination
	M10 - inflorescence meristem at 16 days after germination

Seed development, series 1

All samples of this series were taken at the moment of abscission of the first flower. Before collection, siliques were washed in RNAlater solution in order to remove pollen.

- general view of the inflorescence at the moment of
abscission of the first flower.

SD.y1 - young seeds 1

Seeds from silique 1.

SD.y2 - young seeds 2

Seeds from silique 2.

SD.y3 - young seeds 3

Seeds from silique 3

SD.y4 - young seeds 4

Seeds from silique 4

SD.y5 - young seeds 5

Seeds from silique 5

Seed development, series 2

All samples of this series were taken at the moment when first silique is 1-1.5 cm long
(corresponds to the moment of the abscission of the 8th flower). Before collection, siliques
were washed in RNAlater solution in order to remove pollen.

	SD1 - seeds 1 Seeds from silique 1.
	SD3 - seeds 3 Seeds from silique 3.
	SD5 - seeds 5 Seeds from silique 5.
	SD7 - seeds 7 Seeds from silique 7.

Seed germination.

	SD.d - dry seeds Dry seeds.
	SD.g1 - germinating seeds 1 Seeds at first day after soaking.
	SD.g2 - germinating seeds 2 Seeds at second day after soaking.
	SD.g3 - germinating seeds 3 Seeds at third day after soaking.

Senescent organs.

	IN.sn - senescent internode. First elongated internode (from last rosette leaf to first cauline leaf). Sample was collected when first silique was yellow and ready to open.
	SD.sn1 - Seeds of first yellowing silique. Sample was collected when first silique was yellow and ready to open.
	POD.sn1 - pod of the senescent silique 1. Sample was collected when first silique was yellow and ready to open.
	SL.sn2 - senescent silique 2 Silique 2. Sample was collected when first silique was yellow and ready to open.

Silique development, series 1 (seeds removed)

All samples of this series were taken at the moment when first silique is 1-1.5 cm long. Before
collection, siliques were washed in RNAlater solution in order to remove pollen. For all samples, seeds were removed.

	POD1 - pod of the silique 1 Pod of the silique 1.
	POD3 - pod of the silique 3 Pod of the silique 3.
	POD5 - pod of the silique 5 Pod of the silique 5.
	POD7 - pod of the silique 7 Pod of the silique 7.

Silique development, series 2 (seeds not removed)

All samples of this series were taken at the moment when first silique is 1-1.5 cm long. Before collection, siliques were washed in RNAlater solution in order to remove pollen.

	SL2 - silique 2 Whole silique 2.
	SL4 - silique 4 Whole silique 4.
	SL6 - silique 6 Whole silique 6.
	SL8 - silique 8 Whole silique 8.