How to create a sample annotation file before analysis
Step 1¶
Create a table in Libreoffice or Excel with one or more columns that will uniquely identify each of your sample. For example,
- In a plate reader or qPCR experiment, you will want a plate number column and a well number column for each measured well.
- In a flow cytometry experiment, create a column with the unique specimen number or the unique filename for each sample.
- In a deep sequencing experiment, it will be the unique index for each library.
- In a Western blot, it will be a gel number column and a lane number column.
Step 2¶
Create one meta data column for each biological and technical variable that you are changing in your experiment.
For example:
- you did your experiment with three different gene knockouts
- each knockout had two different fluorescent reporters
- each fluorescent reporter is induced at 3 different concentrations
- there are 3 technical replicates for each strain.
So the metadata columns you will create are:
- knockoutgene
- reporter
- inductionlevel
- replicate
In addition, create a column called samplelabel with a succinct unique name for each sample (see the example below).
Step 3¶
Save the file as sampleannotations.csv by choosing CSV file type and , as field separator.
Important Pointers¶
- Remember that each variable gets a column. For example, if you collected the same sample at different time points, then create a
timepointmetadata column. - You can insert
NAin columns for which the metadata is not applicable – for example, useNAfor an empty well in a plate reader experiment. - Create a
commentcolumn that can include any atypical explanation. - Do not insert spaces, capital letters or non-alphanumeric characters into your annotations file.
Examples¶
sampleannotations.csv for a plate reader experiment¶
| plate | well | knockoutgene | yfpreporter | iptginductionlevel | replicate | comment |
|---|---|---|---|---|---|---|
| 1 | A1 | NA | NA | NA | NA | blank |
| 1 | A2 | sera | tcg | 0 | 1 | |
| 1 | A3 | sera | tcg | 0 | 2 | |
| 1 | A4 | sera | tcg | 0 | 3 | |
| 1 | A5 | sera | tcg | 10 | 1 | |
| 1 | A6 | sera | tcg | 10 | 2 | |
| 1 | A7 | sera | tcg | 10 | 3 | |
| 1 | A8 | sera | tcg | 100 | 1 | |
| 1 | A9 | sera | tcg | 100 | 2 | |
| 1 | A10 | sera | tcg | 100 | 3 | |
| 1 | A11 | NA | NA | NA | NA | blank |
| 1 | A12 | NA | NA | NA | NA | blank |
| 1 | B1 | NA | NA | NA | NA | blank |
| 1 | B2 | sera | agc | 0 | 1 | |
| 1 | B3 | sera | agc | 0 | 2 | |
| 1 | B4 | sera | agc | 0 | 3 | |
| 1 | B5 | sera | agc | 10 | 1 | |
| 1 | B6 | sera | agc | 10 | 2 | |
| 1 | B7 | sera | agc | 10 | 3 | |
| 1 | B8 | sera | agc | 100 | 1 | |
| 1 | B9 | sera | agc | 100 | 2 | |
| 1 | B10 | sera | agc | 100 | 3 | |
| 1 | B11 | NA | NA | NA | NA | blank |
| 1 | B12 | NA | NA | NA | NA | blank |
| 1 | C1 | NA | NA | NA | NA | blank |
| 1 | C2 | serb | tcg | 0 | 1 | |
| 1 | C3 | serb | tcg | 0 | 2 | |
| 1 | C4 | serb | tcg | 0 | 3 | |
| 1 | C5 | serb | tcg | 10 | 1 | |
| 1 | C6 | serb | tcg | 10 | 2 | |
| 1 | C7 | serb | tcg | 10 | 3 | |
| 1 | C8 | serb | tcg | 100 | 1 | |
| 1 | C9 | serb | tcg | 100 | 2 | |
| 1 | C10 | serb | tcg | 100 | 3 | |
| 1 | C11 | NA | NA | NA | NA | blank |
| 1 | C12 | NA | NA | NA | NA | blank |
| 1 | D1 | NA | NA | NA | NA | blank |
| 1 | D2 | serb | agc | 0 | 1 | |
| 1 | D3 | serb | agc | 0 | 2 | |
| 1 | D4 | serb | agc | 0 | 3 | |
| 1 | D5 | serb | agc | 10 | 1 | |
| 1 | D6 | serb | agc | 10 | 2 | |
| 1 | D7 | serb | agc | 10 | 3 | |
| 1 | D8 | serb | agc | 100 | 1 | |
| 1 | D9 | serb | agc | 100 | 2 | |
| 1 | D10 | serb | agc | 100 | 3 | |
| 1 | D11 | NA | NA | NA | NA | blank |
| 1 | D12 | NA | NA | NA | NA | blank |
| 2 | A1 | NA | NA | NA | NA | blank |
| 2 | A2 | serc | tcg | 0 | 1 | |
| 2 | A3 | serc | tcg | 0 | 2 | |
| 2 | A4 | serc | tcg | 0 | 3 | |
| 2 | A5 | serc | tcg | 10 | 1 | |
| 2 | A6 | serc | tcg | 10 | 2 | |
| 2 | A7 | serc | tcg | 10 | 3 | |
| 2 | A8 | serc | tcg | 100 | 1 | |
| 2 | A9 | serc | tcg | 100 | 2 | |
| 2 | A10 | serc | tcg | 100 | 3 | |
| 2 | A11 | NA | NA | NA | NA | blank |
| 2 | A12 | NA | NA | NA | NA | blank |
| 2 | B1 | NA | NA | NA | NA | blank |
| 2 | B2 | serc | agc | 0 | 1 | |
| 2 | B3 | serc | agc | 0 | 2 | |
| 2 | B4 | serc | agc | 0 | 3 | |
| 2 | B5 | serc | agc | 10 | 1 | |
| 2 | B6 | serc | agc | 10 | 2 | |
| 2 | B7 | serc | agc | 10 | 3 | |
| 2 | B8 | serc | agc | 100 | 1 | |
| 2 | B9 | serc | agc | 100 | 2 | |
| 2 | B10 | serc | agc | 100 | 3 | |
| 2 | B11 | NA | NA | NA | NA | blank |
| 2 | B12 | NA | NA | NA | NA | blank |
sampleannotations.csv for a qPCR experiment¶
| well | rt | amplicon | initiation | codonmutation | replicate | template | qpcrlabel | strain |
|---|---|---|---|---|---|---|---|---|
| B03 | yes | gpd | na | na | 1 | 84+1 | 84q11 | scHP15-2 |
| B04 | yes | gpd | ctgc | 5xcgg | 1 | 84+4 | 84q21 | scHP286-1 |
| B05 | yes | gpd | aaaa | 5xcgg | 1 | 84+5 | 84q31 | scHP291-1 |
| B06 | yes | gpd | ctgc | 5xaga | 1 | 84+8 | 84q41 | scHP314-1 |
| B07 | yes | gpd | aaaa | 5xaga | 1 | 84+9 | 84q51 | scHP315-1 |
| B08 | no | gpd | aaaa | 5xaga | 1 | 84-9 | 84q61 | scHP315-1 |
| C03 | yes | yfp | na | na | 1 | 84+1 | 84q12 | scHP15-2 |
| C04 | yes | yfp | ctgc | 5xcgg | 1 | 84+4 | 84q22 | scHP286-1 |
| C05 | yes | yfp | aaaa | 5xcgg | 1 | 84+5 | 84q32 | scHP291-1 |
| C06 | yes | yfp | ctgc | 5xaga | 1 | 84+8 | 84q42 | scHP314-1 |
| C07 | yes | yfp | aaaa | 5xaga | 1 | 84+9 | 84q52 | scHP315-1 |
| C08 | no | yfp | aaaa | 5xaga | 1 | 84-9 | 84q62 | scHP315-1 |
| D03 | yes | gpd | na | na | 2 | 84+1 | 84q11 | scHP15-2 |
| D04 | yes | gpd | ctgc | 5xcgg | 2 | 84+4 | 84q21 | scHP286-1 |
| D05 | yes | gpd | aaaa | 5xcgg | 2 | 84+5 | 84q31 | scHP291-1 |
| D06 | yes | gpd | ctgc | 5xaga | 2 | 84+8 | 84q41 | scHP314-1 |
| D07 | yes | gpd | aaaa | 5xaga | 2 | 84+9 | 84q51 | scHP315-1 |
| D08 | no | gpd | aaaa | 5xaga | 2 | 84-9 | 84q61 | scHP315-1 |
| E03 | yes | yfp | na | na | 2 | 84+1 | 84q12 | scHP15-2 |
| E04 | yes | yfp | ctgc | 5xcgg | 2 | 84+4 | 84q22 | scHP286-1 |
| E05 | yes | yfp | aaaa | 5xcgg | 2 | 84+5 | 84q32 | scHP291-1 |
| E06 | yes | yfp | ctgc | 5xaga | 2 | 84+8 | 84q42 | scHP314-1 |
| E07 | yes | yfp | aaaa | 5xaga | 2 | 84+9 | 84q52 | scHP315-1 |
| E08 | no | yfp | aaaa | 5xaga | 2 | 84-9 | 84q62 | scHP315-1 |
| F03 | yes | gpd | na | na | 3 | 84+1 | 84q11 | scHP15-2 |
| F04 | yes | gpd | ctgc | 5xcgg | 3 | 84+4 | 84q21 | scHP286-1 |
| F05 | yes | gpd | aaaa | 5xcgg | 3 | 84+5 | 84q31 | scHP291-1 |
| F06 | yes | gpd | ctgc | 5xaga | 3 | 84+8 | 84q41 | scHP314-1 |
| F07 | yes | gpd | aaaa | 5xaga | 3 | 84+9 | 84q51 | scHP315-1 |
| F08 | no | gpd | aaaa | 5xaga | 3 | 84-9 | 84q61 | scHP315-1 |
| G03 | yes | yfp | na | na | 3 | 84+1 | 84q12 | scHP15-2 |
| G04 | yes | yfp | ctgc | 5xcgg | 3 | 84+4 | 84q22 | scHP286-1 |
| G05 | yes | yfp | aaaa | 5xcgg | 3 | 84+5 | 84q32 | scHP291-1 |
| G06 | yes | yfp | ctgc | 5xaga | 3 | 84+8 | 84q42 | scHP314-1 |
| G07 | yes | yfp | aaaa | 5xaga | 3 | 84+9 | 84q52 | scHP315-1 |
| G08 | no | yfp | aaaa | 5xaga | 3 | 84-9 | 84q62 | scHP315-1 |
sampleannotations.csv for a flow cytometry experiment¶
| plate | file | strain | stallcodon | ncodonrepeats | stallsites | initiation | gene | gpdmkate2 | citrine | replicate |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Specimen001B2B02001 | by4741 | na | na | na | na | na | no | no | 1 |
| 1 | Specimen001B3B03002 | schp15 | na | na | na | na | na | yes | no | 1 |
| 1 | Specimen001B4B04003 | schp19 | cgg | 6 | 1 | caaa | maxhis3 | yes | yes | 1 |
| 1 | Specimen001B5B05004 | schp20 | aga | 6 | na | caaa | maxhis3 | yes | yes | 1 |
| 1 | Specimen001B6B06005 | schp76 | aga | 5 | na | caaa | pgk1 | yes | yes | 1 |
| 1 | Specimen001B7E07006 | schp91 | cgg | 5 | 5 | caaa | pgk1 | yes | yes | 1 |
| 1 | Specimen001B8B08007 | schp617 | cca | 8 | na | caaa | pgk1 | yes | yes | 1 |
| 1 | Specimen001B9B09008 | schp618 | cca | 8 | na | ccgc | pgk1 | yes | yes | 1 |
| 1 | Specimen001B10B10009 | schp619 | cca | 8 | na | ccaa | pgk1 | yes | yes | 1 |
| 1 | Specimen001B11B11010 | schp620 | cca | 8 | na | ccac | pgk1 | yes | yes | 1 |
| 1 | Specimen001C2C02011 | schp621 | cca | 8 | na | ccga | pgk1 | yes | yes | 1 |
| 1 | Specimen001C3C03012 | schp622 | cca | 8 | na | ctgc | pgk1 | yes | yes | 1 |
| 1 | Specimen001C4C04013 | schp623 | cca | 8 | na | aaaa | pgk1 | yes | yes | 1 |
| 1 | Specimen001C5C05014 | schp624 | cca | 8 | na | acgc | pgk1 | yes | yes | 1 |
| 1 | Specimen001C6C06015 | schp625 | cca | 8 | na | ctg | pgk1 | yes | yes | 1 |
| 1 | Specimen001C7C07016 | schp626 | ccg | 8 | 1 | caaa | pgk1 | yes | yes | 1 |
| 1 | Specimen001C8C08017 | schp627 | ccg | 8 | 1 | ccgc | pgk1 | yes | yes | 1 |
| 1 | Specimen001C9C09018 | schp628 | ccg | 8 | 1 | ccaa | pgk1 | yes | yes | 1 |
| 1 | Specimen001C10C10019 | schp629 | ccg | 8 | 1 | ccac | pgk1 | yes | yes | 1 |
| 1 | Specimen001C11C11020 | schp630 | ccg | 8 | 1 | ccga | pgk1 | yes | yes | 1 |
| 1 | Specimen001D2D02021 | schp631 | ccg | 8 | 1 | ctgc | pgk1 | yes | yes | 1 |
| 1 | Specimen001D3D03022 | schp632 | ccg | 8 | 1 | aaaa | pgk1 | yes | yes | 1 |
| 1 | Specimen001D4D04023 | schp633 | ccg | 8 | 1 | acgc | pgk1 | yes | yes | 1 |
| 1 | Specimen001D5D05024 | schp634 | ccg | 8 | 1 | ctg | pgk1 | yes | yes | 1 |
| 2 | Specimen002E2E02001 | by4741 | na | na | na | na | na | no | no | 2 |
| 2 | Specimen002E3E03002 | schp15 | na | na | na | na | na | yes | no | 2 |
| 2 | Specimen002E4E04003 | schp19 | cgg | 6 | 1 | caaa | maxhis3 | yes | yes | 2 |
| 2 | Specimen002E5E05004 | schp20 | aga | 6 | na | caaa | maxhis3 | yes | yes | 2 |
| 2 | Specimen002E6E06005 | schp76 | aga | 5 | na | caaa | pgk1 | yes | yes | 2 |
| 2 | Specimen002E7E07006 | schp91 | cgg | 5 | 5 | caaa | pgk1 | yes | yes | 2 |
| 2 | Specimen002E8E08007 | schp617 | cca | 8 | na | caaa | pgk1 | yes | yes | 2 |
| 2 | Specimen002E9E09008 | schp618 | cca | 8 | na | ccgc | pgk1 | yes | yes | 2 |
| 2 | Specimen002E10E10009 | schp619 | cca | 8 | na | ccaa | pgk1 | yes | yes | 2 |
| 2 | Specimen002E11E11010 | schp620 | cca | 8 | na | ccac | pgk1 | yes | yes | 2 |
| 2 | Specimen002F2F02011 | schp621 | cca | 8 | na | ccga | pgk1 | yes | yes | 2 |
| 2 | Specimen002F3F03012 | schp622 | cca | 8 | na | ctgc | pgk1 | yes | yes | 2 |
| 2 | Specimen002F4F04013 | schp623 | cca | 8 | na | aaaa | pgk1 | yes | yes | 2 |
| 2 | Specimen002F5F05014 | schp624 | cca | 8 | na | acgc | pgk1 | yes | yes | 2 |
| 2 | Specimen002F6F06015 | schp625 | cca | 8 | na | ctg | pgk1 | yes | yes | 2 |
| 2 | Specimen002F7F07016 | schp626 | ccg | 8 | 1 | caaa | pgk1 | yes | yes | 2 |
| 2 | Specimen002F8F08017 | schp627 | ccg | 8 | 1 | ccgc | pgk1 | yes | yes | 2 |
| 2 | Specimen002F9F09018 | schp628 | ccg | 8 | 1 | ccaa | pgk1 | yes | yes | 2 |
| 2 | Specimen002F10F10019 | schp629 | ccg | 8 | 1 | ccac | pgk1 | yes | yes | 2 |
| 2 | Specimen002F11F11020 | schp630 | ccg | 8 | 1 | ccga | pgk1 | yes | yes | 2 |
| 2 | Specimen002G2G02021 | schp631 | ccg | 8 | 1 | ctgc | pgk1 | yes | yes | 2 |
| 2 | Specimen002G3G03022 | schp632 | ccg | 8 | 1 | aaaa | pgk1 | yes | yes | 2 |
| 2 | Specimen002G4G04023 | schp633 | ccg | 8 | 1 | acgc | pgk1 | yes | yes | 2 |
| 2 | Specimen002G5G05024 | schp634 | ccg | 8 | 1 | ctg | pgk1 | yes | yes | 2 |
sampleannotations.csv for a deep sequencing experiment¶
| index | samplename | genotype | treatment | type | replicate |
|---|---|---|---|---|---|
| GTAGCC | wtuntreatedmono | wt | untreated | mono | 1 |
| AAGCTA | wtifnmono | wt | ifn | mono | 1 |
| GCCTAA | rack11untreatedmono | rack1 | untreated | mono | 1 |
| CGTGAT | rack11ifnmono | rack1 | ifn | mono | 1 |
| GATCTG | rack12untreatedmono | rack1 | untreated | mono | 2 |
| ATTGGC | rack12ifnmono | rack1 | ifn | mono | 2 |
| CACGAT | wtuntreatedtotal | wt | untreated | total | 1 |
| CAACTA | wtifntotal | wt | ifn | total | 1 |
| GGTAGC | rack11untreatedtotal | rack1 | untreated | total | 1 |
| GTAGAG | rack11ifntotal | rack1 | ifn | total | 1 |
| CAAAAG | rack12untreatedtotal | rack1 | untreated | total | 2 |
| ATGAGC | rack12ifntotal | rack1 | ifn | total | 2 |