Plate editor: laying out a qPCR plate by hand

The Plate editor is a free Clarida tool for laying out samples and assays on 96- and 384-well plates. This page describes how to place them one well, one replicate group or a whole set at a time, and how to check, correct and export the layout.

The Plate editor is a free Clarida tool for laying out samples and assays on 96- and 384-well plates. It needs no account, and your plates are kept in your browser.

The editor places what you choose, where you click; it does not design the layout for you. In the qPCR app, Run layout generates a complete layout from four settings in its Auto and Assisted modes, as described in Plate layout generation, and in its Manual mode changes wells one at a time in a table. The editor's Set level uses the same settings on the samples and assays you tick, from the well you click. When a plate is ready, Create new qPCR experiment starts an experiment with the layout in place. The editor does not analyze data.

This page has two parts. How to covers laying out a plate, step by step. How it works explains the rules behind each step; read it when a step raises a question. The running example is a lab that measures the relative expression of IL6 and TNF in macrophages by RT-qPCR: three control cultures (Ctrl-1 to Ctrl-3) and three treated ones (Treated-1 to Treated-3) as biological replicates, GAPDH and ACTB as reference genes, a no-template control (NTC) and a no-reverse-transcription control (No-RT). Every sample is measured with every assay in three technical replicates on one 96-well plate: 8 samples × 4 assays × 3 wells, exactly 96 wells.

1. Add your samples and assays

Open the plate editor at app.clarida.bio/plate-editor. The Plate layout section holds the editor: the Samples and Assays lists on the left and the plate on the right. The panel at the right of the page has two tabs, Help and Checks.

Under each list is an add row. Choose the type with the code chip (X ▾), type a name in Add or paste samples… (or Add or paste assays…) and press Enter or Add sample. To add many at once, paste several lines into the field, or use the clipboard button, Paste a list of samples: one name per line, with the type in a second column when you paste two columns from Excel. A line such as NTC, No-RT or Std becomes a sample of that type; Add to list adds them. Our lab pastes its eight sample names, then its four assays, with "Reference gene" in the second column for GAPDH and ACTB.

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Each row's ⋯ menu has Rename…, Type and Delete. Deleting an item also clears it from every well that holds it, with Undo in the message that follows. An item without a type is listed under ? with a note to set it.

If the layout already exists, start from the Import section above the editor instead:

• Import file reads the layout from an RDML, QuantStudio, Bio-Rad CFX or LightCycler 480 run file, or from a CSV or Excel file the plate editor exported. It replaces everything in the editor, after Replace everything? asks first.
• Paste samples and Paste assays take an 8 × 12 or 16 × 24 block of cells copied from Excel, one with the sample names and one with the assay names. Fill either or both, then Place on Plate 1 places them on that plate; with more plates, the arrow next to it chooses another.

Either can be undone once from its message.

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See Type codes and colors and Where your plates are kept.

2. Place wells one at a time

On a first visit the editor opens with Place and Well: one click places one well. While the plate is empty, a note on it says what to do. Click a sample in Samples and an assay in Assays to pick them (a second click unpicks), then click wells. The pick stays until you change it, and each tab shows what is picked under its name. Drag across wells to fill a box, click a row letter or a column number to fill that row or column, and click the corner ◢ to fill the whole plate.

Our lab picks Ctrl-1 and IL6 and clicks A1, A2 and A3.

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Hovering a well previews what the click would do, and the line under the plate says it in words. A well that holds another sample or assay is overwritten; the preview marks it in red first.

See Tools and levels and What a drag means.

3. Place replicate groups

Switch to Replicates: one click now places a replicate group of the pick, starting at the well you click. Open Placement to set Replicates (1 to 6) and the Replicate direction: Side by side puts the group along the row from the clicked well, Stacked puts it down the column. The Placement button shows the current choice in words, for example "3× side by side".

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To place a single well without leaving Replicates, Alt-click it (Alt+Enter from the keyboard), or switch to Well (W).

See Where a placement goes and Replicate groups and their numbers.

4. Place the whole set in one click

Switch to Set. The lists now have tick boxes: All at the top, one per type group, and one per item. Ctrl-click or Shift-click a name to tick or untick it; a plain click ticks only that item. Tick the samples and assays to place; their order in the list is the order on the plate, and you can drag the ⋮⋮ grip to change it within its type group. Click the start well.

Our lab ticks All samples and All assays and clicks A1. With Block by Assay, 3×, Fill order Down and Rectangular blocks, the plate fills completely: one block of 8 × 3 wells per assay, each sample in its own row, its three technical replicates side by side.

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See How Set lays out the set.

5. Move and clear wells

Move drags wells to another place; Clear empties them. Both work at the current level: at Well a single well (or a box you drag across), at Replicates the whole replicate group, at Set the block under the pointer. With Move or Clear, the toolbar adds Both, Sample and Assay, which choose what is moved or cleared; the other half of each well stays where it is.

• Move: drag a well onto an empty one to move it, onto a filled one to swap the two. Hold Alt when you drop to copy instead.
• Clear: click a well, a group or a block. Before you click, a red dashed outline shows what would be cleared, and the line under the plate says it in words. A row letter or a column number clears that row or column, and ◢ clears the plate.
• The eraser: in Clear, every item with wells on the open plate gets an eraser next to its well count. Hovering it turns it red and outlines the item's wells in red; a click clears them all.

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Every change can be undone: Undo and Redo sit in the section header (Ctrl+Z, Ctrl+Shift+Z), and a change of many wells also has Undo in its message.

See Tools and levels and What a drag means.

6. Work with several plates and 384-well quadrants

The plate strip above the plate has one tab per plate. Add a plate adds one of 96 or 384 wells; one plate set can hold both, and then each tab also shows its format. Click the open plate's tab for its menu: the plate's name, Rename…, its format (96 or 384 wells), Clear and Delete. Clear and Delete have Undo in their message. A plate loaded from a run file keeps the file's name, which exports use; the tab itself still reads Plate 1, Plate 2 and so on. Two plates cannot share a name.

A placement that does not fit continues on the next plate, as long as that plate has the same format. If there is no such plate, the preview turns red and the click does nothing: add a plate with + and the placement continues there.

On a 384-well plate, the strip adds Full and Q1 to Q4: Full shows all 384 wells, Q1 to Q4 show one quadrant at a time as a 96-well plate. In a quadrant, the editor places as on a 96-well plate and continues in the next quadrant. Our lab, moving to 384 wells, opens Q1 and places its set from A1: the same 96 wells, on every other row and column.

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See Where a placement goes.

7. Check the layout

Open the Checks tab in the panel on the right. It looks at the open plate for Wells with only a sample or an assay, Missing sample–assay pairs, Assays without a negative control, Inconsistent replicate counts and Names that look alike, lists only the ones that find something, and reads All checks passed when none does. Click a check to see what it found and mark its wells. A plate with something to check shows the number on its tab; clicking the number opens that plate's checks.

To read the layout well by well, switch View to Labeled squares (or press D): each well then shows its sample and assay by name, with its replicate number, instead of the codes. Our lab checks its plate this way before the run.

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See The checks and Type codes and colors.

8. Export the layout

The Export section below the editor has three cards:

• Copy: Copy table and Copy plate map.
• Download: choose CSV, Excel, RDML or Instrument, then download.
• Clarida: Save to Clarida keeps the plate set in your Clarida workspace, My plates lists the ones you saved, and Create new qPCR experiment starts an experiment with the layout in place, after asking first.

Copy and CSV work without an account; the others need a free one. Every button can be clicked: without an account it asks you to sign in, and the plate comes along.

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See Export formats and Where your plates are kept.

Tools and levels

Three tools say what a click does; three levels say how much it affects. The level applies to every tool:

With Clear, at any level, a row or column label clears the line and ◢ clears the plate (or the quadrant on view). With Move and Clear, Both, Sample and Assay choose which half of each well they act on.

• Replicate group: the wells on the plate with the same sample and the same assay: its technical replicates. Biological replicates are separate samples (Ctrl-1, Ctrl-2, Ctrl-3) and so separate groups.
• Block: touching wells that share an assay, or a sample when Block by is Sample. Each block is outlined on the plate, and the outline follows every change: moving wells out of a block shrinks or splits it.
• Pick: what the next Place click puts down. At Well and Replicates it is one sample and one assay, or only one of the two; at Set it is the ticked items.

The level you used last is kept for your next visit; the tool always starts at Place. In Move and Clear the lists hide the pick, so a click cannot change it unseen: a list click in Move switches to Place, and in Clear it does nothing.

The editor suggests a level when you seem to need one: after placing the same item three times in a line it offers Replicates, after three replicate groups in a row it offers Set. Each suggestion appears once. Accepting Replicates also sets the Replicate direction that repeats your line: three wells along a row give Side by side (the suggestion reads "3× side by side"), three down a column give Stacked ("3× stacked").

What a drag means

What a drag does depends on where it starts:

• A name in a list: drop it onto a well, the same as clicking the name, then the well. A drop places what a click would at the current level, and it keeps the pick on the other list: dropping IL6 while Ctrl-1 is picked places Ctrl-1 with IL6. At Set, the dropped item joins the ticked items. At Well, a row or column label or ◢ takes a drop too and fills the line or the plate; at Replicates and Set only a well does, because a group or a set needs a start well.
• The ⋮⋮ grip: reorder the list, within the item's type group.
• A well: a box (Place fills it, Clear empties it, Move selects it when the drag starts on an empty well), or in Move, starting on a filled well, move that well.

After your first drop the editor shows, once, that clicking works too: a picked item stays picked, so you can click well after well.

Where a placement goes

Every placement follows one rule: start at the clicked well, continue at the top of the next column (or, when the placement runs along the rows, at the start of the next row), then on the next plate. The next plate must exist and have the same format; otherwise the preview is red and the click does nothing. The line under the plate says how many wells would land past the last plate and how to continue: add a plate with +, and the placement continues there (or, when the next plate has the other format, it says so). A placement that continues on the next plate is one change and one Undo.

On a 384-well plate the view decides. In Full, placing runs down all 16 rows. In Q1 to Q4, the quadrant is placed as a 96-well plate and a placement continues in the next quadrant, as if the four quadrants were consecutive plates. On a 384-well plate, Placement adds 384 quadrants, whose 384 quadrant style decides which wells make up a quadrant:

• Interleaved: every other row and column, the wells a multichannel pipette with 96-well (9 mm) tip spacing reaches (Q1 = A1, A3, C1 …).
• Corner blocks: the four 96-well quarters of the plate (Q1 = A1–H12).

Move never reads the Placement settings; it moves what it sees. At Replicates, a replicate group whose wells follow each other down the columns (or along the rows) moves as a run, in its own order, and may continue on the next plate. Everything else (a block, a box, scattered wells) moves as a fixed shape and is refused at the plate's edge.

How Set lays out the set

Set uses the same layout routine and the same settings Clarida uses to generate a whole plate layout: Block by, Fill order, Block style, Replicate placement and Plate crossing. Fill order decides how a Set fills the plate: Down fills down the columns, then the next column; Across fills along the rows. The settings are explained in Plate layout generation. Two things differ:

• What is placed: only the ticked samples × assays, in the order the list shows them, instead of every sample × assay. The list groups items by type code, so all genes of interest come before the reference genes, for example.
• Where it starts: at the well you click, instead of A1. With Rectangular blocks, the first block starts at that well and every later block starts on a fresh column (or row).

Replicates is the number of technical replicates, that is wells, per sample × assay, used at Replicates and Set. Only one of Replicate direction and Fill order applies at a time: Replicate direction at Replicates; at Set, Fill order and Replicate placement decide where replicates go. Fill order, Block style, Replicate placement and Plate crossing apply at Set only; at Replicates they keep their defaults whatever you chose for Set, so a group's replicates are always adjacent and a group may continue on the next plate. Plate crossing decides whether a block may continue on the next plate (Split across plates) or is kept whole on one plate (Keep blocks whole).

Placement shows only the settings the current tool and level use. At Well, Move and Clear, a single line says why there is little to set; at Set, the pattern settings are grouped under Set pattern. The button itself sums up the choice in words, such as "3× side by side" or "3× fill down".

The preview follows every change in Placement while the popover is open, so you can try a setting on the plate before you click. Placing a sample × assay that already has wells is allowed; the line under the plate says so first ("Treated-1 · IL6 already has 3 wells: this adds 3 more").

Replicate groups and their numbers

Each well of a replicate group shows its replicate number (which technical replicate it is) under its code; a sample × assay with a single well shows none. Wells placed by one click at Replicates or Set form one replicate group, numbered 1, 2, 3 in the order the click placed them. Wells placed one at a time are numbered within their sample × assay in plate order, row by row.

Type codes and colors

Every sample and assay gets a code: a type letter and a number. The letter comes from the type you chose, and the same letters are used on both lists:

Each list is grouped by code, under a heading such as X · Unknown or N · Should not amplify. The number is the item's position within its group, so reordering the group renumbers the codes. An item without a type shows ?.

View sets how the plate looks:

• Well shape: Circles show each well's code; Labeled squares show the names instead, so the plate reads without relying on color. D switches between the two.
• Colors: one of three palettes. Clarida codes gives one hue per code, and a lighter or darker shade per item, in list order. Color-blind safe uses the Okabe–Ito hues, which stay distinguishable with the common color-vision deficiencies. Classic gives one color per item in list order, as in Clarida's other plates.

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The well's fill shows one list and the block outline the other: with Block by Assay, the outline and tint show the assay and the well shows the sample. To give one item its own color, click its code chip in the list:

• A shade of the palette: the popover shows the six shades of every code in the palette in use (Classic shows its own colors). A shade follows the palette: switch from Clarida codes to Color-blind safe and the item takes the same shade in the new hues.
• Custom color: any color, from the color picker that opens below the shades. The list and the plate show it while you choose; it stays the same in every palette.
• Default color gives the item its palette color back. Reset N custom colors under Colors in View does that for every item at once.

Every color is allowed. A color close to the red that marks overwrites and Clear gets a warning, because previews on its wells may be hard to read. Each choice is one step for Undo.

The checks

The checks look at the open plate:

A standard series or an NTC run for one assay only shows up under Missing sample–assay pairs, once for each other assay. That is on purpose: the check cannot tell a planned gap from a forgotten one, so it lists them and leaves the call to you. Clicking it marks every well of the samples involved, so you can see where to add the missing ones.

The Checks tab lists only the checks that find something. A click on a check opens it, lists what it found and marks exactly its wells; Esc or a second click clears the mark. The tab of every plate with something to check carries the count, which pulses when it goes up; the first time, a note explains it. The checks only flag; they change nothing.

Keyboard

Every pointer action has a keyboard path. The letters work while the editor has focus and no text field does, and never with Ctrl, ⌘ or Alt held. ? lists them all.

In the plate strip, ← and → open the previous and next plate, and Enter opens the open plate's menu. In a list, focus a ⋮⋮ grip and press Space to pick the item up, ↑ and ↓ to move it within its group, Space to drop it and Esc to cancel.

Where your plates are kept

The plates, the lists and your settings are kept in this browser on this device, and saved as you work: closing the tab loses nothing. A private window, or a browser with storage turned off, keeps nothing; the editor says so above the plate. With the editor open in two tabs, the last change wins, and a notice in each tab says so.

The layout leaves the browser only when you ask for it:

• Import file sends the file to Clarida to be read; it is not kept.
• The CSV, Excel, RDML and Instrument downloads are written by Clarida, so the layout is sent to produce the file. Copy and the pasted plate maps stay in the browser.
• Signing in from an option that needs an account takes the plate along through the sign-in, also when the sign-in link opens on another device, for up to 24 hours.
• Save to Clarida and Create new qPCR experiment keep the layout in your workspace. Your saved plate sets are also on the Saved plates page, under Plate editor in the left navigation, where you can open, rename or delete them.

Export formats

The CSV and Excel files load back through Import file: wells, samples with their types, assays, replicates and plate names return as they were written. Assay targets, dyes and items no well uses are not in those files and do not come back.

• Copy: tab-separated text for Excel, a lab notebook or an instrument's import window. Copy table copies the well table, Copy plate map the plate as a grid. With more than one plate, choose This plate or All plates first; all plate maps come one after another, each under its plate name.
• CSV: one row per well, with well, sample, sample type, assay and replicate.
• Excel: a workbook with a plate map and a well table for each plate.
• RDML: the open qPCR data standard, read by most qPCR software.
• Instrument: a plate setup file to load into the instrument software, one plate per file. Choose the Instrument, the plate and a dye per assay (SYBR unless you choose another). Check file shows what the file changes or cannot hold; the download follows the check.

The Download card remembers the format you chose last.