Frequently Asked Questions
Can you share the codes to reproduce databrowsers locally for in house data?
You can find codes for the ImmGen projects on github: https://github.com/Immgen
How is the W-plot created in MyGeneSet?
The W-plot in MyGeneSet is calculated based on the average expression values from each population, not from each replicate. v The values in W-plot are log2 (gene expression value/average expression value of all the selected populations).
Does ImmGen have APIs to access the data?
Yes, we have APIs (http://rstats.immgen.org/Skyline/api/docs/) for RNAseq Gene Skyline to retrieve the expression values and plots without using the graphical user interface of the web page.
How do I find out more information about each profiled cell type?
On our 'microarray' and 'RNAseq' data browsers, many of the population names are hyperlinked to a pdf file containing the gating strategies used.
Is it possible to get the raw data (fastq) from some dataset?
All the raw fastq files can be downloaded from GEO (e.g. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109125). Please check the 'SRA Run Selector' at the end of the webpage. You can also use NCBI SRA Toolkit to fetch the data directly from NCBI. Here's the documentation: https://github.com/ncbi/sra-tools/wiki
How can I cite the use of ImmGen datasets?
If these data were of value to you, we would be grateful if you could mention ImmGen in the acknowledgments of publications that were enriched by these data (for example: “This work benefitted from data assembled by the ImmGen consortium”), and/or quote the primary ImmGen reference: Heng TS, et al, Immunological Genome Project Consortium. Nat Immunol. 2008 10 : 1091.
Where can I find Immgen datasets?
Please check here to download all the published ImmGen datasets: http://rstats.immgen.org/DataPage/
Is the ImmGen database available for commercial use?
ImmGen data are completely public.
What is the difference between V1 and V2 dataset in microarray gene skyline?
The ImmGen V2 datasets was generated using a different set of amplification reagents (Ambion WT Expression Kit, not the Affymetrix GeneChip WT cDNA Synthesis and Amplification Kits).
Both V1 and V2 ImmGen datasets use the same Affymetrix Array (Affymetrix Mouse Gene 1.0 ST Array).
V1 and V2 results are very similar but do show some differences, and can NOT properly be compared or normalized to one another using standard normalization. V1 and V2 datasets have some overlapped cell types.
What is the scale unit used in the Gene Skyline databrowser, Is the data normalized?
The expression values shown in the Gene Skyline are normalized by DESeq2.
Here's a description of the common normalization methods in RNAseq analysis : https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html As such, they do not have a precise scale ( like " transcription per Million, TPM), although in practice they are not far from TPM.
Suggestions for improvements on the data presentation are welcome, as are suggestions of cell-types or states that are missing from the databrowsers and would be useful to you.
Please email us at ImmGen-at-hms.harvard.edu
You can find codes for the ImmGen projects on github: https://github.com/Immgen
How is the W-plot created in MyGeneSet?
The W-plot in MyGeneSet is calculated based on the average expression values from each population, not from each replicate. v The values in W-plot are log2 (gene expression value/average expression value of all the selected populations).
Does ImmGen have APIs to access the data?
Yes, we have APIs (http://rstats.immgen.org/Skyline/api/docs/) for RNAseq Gene Skyline to retrieve the expression values and plots without using the graphical user interface of the web page.
How do I find out more information about each profiled cell type?
On our 'microarray' and 'RNAseq' data browsers, many of the population names are hyperlinked to a pdf file containing the gating strategies used.
Is it possible to get the raw data (fastq) from some dataset?
All the raw fastq files can be downloaded from GEO (e.g. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109125). Please check the 'SRA Run Selector' at the end of the webpage. You can also use NCBI SRA Toolkit to fetch the data directly from NCBI. Here's the documentation: https://github.com/ncbi/sra-tools/wiki
How can I cite the use of ImmGen datasets?
If these data were of value to you, we would be grateful if you could mention ImmGen in the acknowledgments of publications that were enriched by these data (for example: “This work benefitted from data assembled by the ImmGen consortium”), and/or quote the primary ImmGen reference: Heng TS, et al, Immunological Genome Project Consortium. Nat Immunol. 2008 10 : 1091.
Where can I find Immgen datasets?
Please check here to download all the published ImmGen datasets: http://rstats.immgen.org/DataPage/
Is the ImmGen database available for commercial use?
ImmGen data are completely public.
What is the difference between V1 and V2 dataset in microarray gene skyline?
The ImmGen V2 datasets was generated using a different set of amplification reagents (Ambion WT Expression Kit, not the Affymetrix GeneChip WT cDNA Synthesis and Amplification Kits).
Both V1 and V2 ImmGen datasets use the same Affymetrix Array (Affymetrix Mouse Gene 1.0 ST Array).
V1 and V2 results are very similar but do show some differences, and can NOT properly be compared or normalized to one another using standard normalization. V1 and V2 datasets have some overlapped cell types.
What is the scale unit used in the Gene Skyline databrowser, Is the data normalized?
The expression values shown in the Gene Skyline are normalized by DESeq2.
Here's a description of the common normalization methods in RNAseq analysis : https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html As such, they do not have a precise scale ( like " transcription per Million, TPM), although in practice they are not far from TPM.
Suggestions for improvements on the data presentation are welcome, as are suggestions of cell-types or states that are missing from the databrowsers and would be useful to you.
Please email us at ImmGen-at-hms.harvard.edu