The MGA Data Repository

Data Type	Human	Mouse	Rat	Rhesus Macaque	Dog	Chicken	Zebra fish	Bee	Fruit Fly	Water Flea	Worm	Baker's Yeast	Fission Yeast	Arabidopsis	Corn	Malaria Parasite	Total
ChIP-seq	8248	758	4	5	11	14	34	-	514	18	198	527	405	212	12	52	11012
ChIP-seq-invitro	-	-	-	-	-	-	-	-	-	-	-	-	931	-	-	-	931
ChIP-seq-peak	8206	28	-	-	-	-	-	-	-	-	-	-	-	-	-	-	8234
Transcription Profiling	2431	1352	13	15	12	33	12	16	371	11	19	22	16	13	8	13	4357
DNase FAIRE etc.	1434	42	-	-	-	-	4	-	68	-	6	58	8	9	3	12	1644
DNA methylation	24	4	-	-	-	-	-	-	-	-	-	-	-	-	-	-	28
Genome annotation	32	23	2	2	2	15	6	2	16	4	18	4	5	5	3	3	179
Sequence-derived	3617	2315	-	-	-	1	14	9	1240	-	9	9	9	1531	9	-	8764
Total # of Samples	27051	4535	19	22	25	63	70	27	2209	33	250	620	443	2701	35	15	38185

Data types are the following:

• ChIP-seq: raw data (reads mapping coordinates) from classical ChIP-seq experiments targeting transcription factors, protein-DNA interaction, histone variants and modifications, etc.
• ChIP-seq-invitro: raw data (reads mapping coordinates) from in-vitro ChIP-seq experiments such ad DAP-seq.
• ChIP-seq-peak: peak regions provided by the authors of the data
• Transcript Profiling: raw data from experiments aimed at profiling transcripts initiation such as CAGE, GRO-cap, GRO-seq, PEAT, etc.
• DNase FAIRE etc.: raw data from chromatin and chromatin accessibility studies such as MNase-seq, DNase-seq, DNase-hypersensitivity, etc.
• DNA methylation: raw data from methylation studies.
• Genome Annotation: transcription start sites, transcription end sites, intron-exon boundaries
• Sequence derived: PWM matches, Natural Variants, Conservation scores, etc.

The list of series present in the database can be found in the MGA Data Overview page.

Sample name conventions

Samples names in MGA contain useful information about the samples' biological and technical variables. For example, the sample '* S2|PolII|80mMsalt|control' contains some information that can be summarised in the figure below: Sample names are divided into multiple sections separated by pipes ('|') or sometimes by dash lines ('-'). Each section is devoted to store information about one important sample variable:

1. Cell type: the cell in which the sample experiment was carried out. This can refer to a cell line (for example GM12878), a developmental stage (as in the example of a S2 cell in D. melanogaster) or a mutant strain (for example 'WT', for wild type cells, or 'anchor-away Abf1', for cell depleted of Abf1 TF).
2. Target: target protein that is the focus of the sample. Examples are transcription factors (CTCF, YY1, etc.), DNA-interacting proteins ('PolII', histones, etc.), histone modifications and variants (H3K4me3, H2A.Z, etc.).
3. Conditions: important conditions in which the experiment was performed and that characterise one or more samples. Examples can be specific growing media or time points during a time course experiment. Note that this field does not list growing conditions that are common to all samples in the series.
4. Additional Info: other information that characterise the samples such as replica number
5. Star: the star symbol ('*') at the beginning of the name indicates that this sample has unoriented features. This is often the case for samples containing peak lists (a peak in the genome is unoriented by definition) or samples derived from paired-end sequencing (the fragment defined by the two paired reads does not have a preferred orientation in the genome).

Note that the first two fields are always present in the sample name, whereas the others can be missing if non-relevant.