Latest improvements for QIAGEN OmicSoft Lands
ArchiveQIAGEN OmicSoft Lands
Release date: 2024-02-01
OmicSoft Lands Release 2024R2
Highlights
- Extended gene annotations enable new gene selection strategies
- New proteomics projects in ClinicalProteomicTumor Land
- Hundreds of new datasets for human, mouse, and rat
- Updates to ATCC Cell Line Lands
General updates
In OmicSoft Studio v12.8, gene annotations for Human and Mouse Lands include dozens of new fields that describe gene function, cellular location, inhibitors and activators, and tissue specificity. Learn more at this knowledge page.
OncoLand updates
Figure 1. New samples in OncoHuman and ClinicalProteomicTumor, grouped by DiseaseCategory.
ClinicalProteomicTumor
This release adds 643 samples and 563 comparisons from 3 datasets, focused on endometrial carcinoma, head and neck squamous cell carcinoma, and lung squamous cell carcinoma.
In addition, we integrate metadata from pan-cancer analyses from PubMed IDs 37582339, 38359819, 37582357, and 37582358, supporting the generation of 840 new statistical comparisons, including new comparison type primary tumor versus paired adjacent normal tissue.
Figure 2. In ClinicalProteomicTumor dataset PDC000125, differential expression at the RNA (top) and protein (bottom) level, comparing primary tumors (endometrial carcinoma) versus paired adjacent normal tissue.
OncoHuman
This release adds 7784 samples and 1254 comparisons from 106 datasets, including studies on:
- Chronic myeloid leukemia: GSE97562 and GSE52362
- Acute lymphoblastic leukemia: GSE200864, GSE240296, GSE240261, GSE131184, GSE78234, and GSE159506
- Chronic lymphocytic leukemia: GSE145847, GSE126595, GSE125791, GSE80355, and GSE80355
- Diffuse large B-cell lymphoma: GSE155398, GSE158120, GSE185796, and GSE103265
- Follicular lymphoma: GSE148656 and GSE152068
- Mantle cell lymphoma: GSE214725
- Multiple myeloma: GSE164706, GSE164701, GSE235356, and GSE89511
- Plasma cell leukemia: GSE164703
- T-cell lymphoma: GSE168557, GSE169644, GSE169644, and GSE160817
- Waldenström macroglobulinemia: GSE171739, GSE139671, and GSE70511
- Acute promyelocytic leukemia: GSE172057, GSE51082, GSE51082, and GSE188608
- Acute myelogenous leukemia: GSE114868, GSE171053, GSE103344, GSE161532, GSE222616, and GSE97331
- Cutaneous T-cell lymphoma: GSE17601
- Squamous cell carcinoma: GSE117973, GSE84713, and GSE108061
- Urinary cancer (kidney, bladder, and urothelial): GSE186691, GSE252406, GSE201395, GSE12606, GSE1982, GSE1982, GSE252629, GSE252600, GSE244498, GSE235908, GSE228525, GSE223069, GSE216494, and GSE216494
- Female reproductive cancer (breast, ovary, and endometrium): GSE180508, GSE47994, GSE187008, GSE114082, GSE20181, GSE26304, GSE76040, GSE247667, GSE169617, GSE169659, and GSE222291
- Lung cancer: GSE6044, GSE63074, GSE235048, GSE190141, GSE45626, GSE152529, GSE160482, GSE43580, and GSE207471
- Blastic plasmacytoid dendritic cell neoplasm: GSE185982, GSE184656, GSE164939, GSE112210, and GSE112209
- Colorectal and liver cancer: GSE119409, GSE43841, GSE45270, GSE46513, GSE79460, GSE79461, GSE95132, GSE26027, GSE215011, and GSE92528
- Medulloblastoma and adrenocortical carcinoma: GSE21140 and GSE90713
- Male urogenital cancer (testis and prostate): GSE262137 and GSE32571
- Glioblastoma: GSE244666, GSE223607, GSE218860
- Melanoma: GSE208004, GSE212219, GSE57445, GSE140394, GSE104849, GSE43260, GSE202687, GSE218004, GSE192564, GSE59455, GSE238207, and GSE215750
Removed/reprocessed datasets or comparisons
GSE5462 was removed and replaced by GSE20181.
As part of the standard review process, comparisons and/or metadata for the following already-landed projects were revised
and can be found by an updated OSModifiedDate “2024R2”.
Full project list
GSE103265, GSE103344, GSE104849, GSE108061, GSE112209, GSE112210, GSE114082, GSE114868, GSE117620, GSE117973, GSE119409, GSE122773, GSE125791, GSE12606, GSE126595, GSE131184, GSE139671, GSE140394, GSE145847, GSE148656, GSE152068, GSE152529, GSE155398, GSE158120, GSE159506, GSE160482, GSE160817, GSE161532, GSE164701, GSE164703, GSE164706, GSE164939, GSE165612, GSE168557, GSE169617, GSE169644, GSE169659, GSE171053, GSE171739, GSE172057, GSE17601, GSE180508, GSE184656, GSE185796, GSE185982, GSE186691, GSE187008, GSE188608, GSE190141, GSE192564, GSE1982, GSE200864, GSE201395, GSE20181, GSE202687, GSE207471, GSE208004, GSE21140, GSE212219, GSE214725, GSE215011, GSE215750, GSE218004, GSE222291, GSE222616, GSE228419, GSE229611, GSE234673, GSE235048, GSE235356, GSE235662, GSE238207, GSE240261, GSE240296, GSE245488, GSE250442, GSE26027, GSE26304, GSE32571, GSE43260, GSE43580, GSE43841, GSE45270, GSE45626, GSE46513, GSE47994, GSE51049, GSE51082, GSE52362, GSE57445, GSE59455, GSE6044, GSE63074, GSE70511, GSE76040, GSE78234, GSE79460, GSE79461, GSE80355, GSE84713, GSE89511, GSE90713, GSE92528, GSE95132, GSE97331, GSE97562
DiseaseLand updates
Figure 3. New samples in HumanDisease, MouseDisease, and RatDisease, grouped by DiseaseCategory.
HumanDisease
This release adds 3625 samples and 1086 comparisons from 90 datasets, including studies on:
- Aging: GSE121444 and GSE6348
- Neurodegenerative disorder: GSE122063 and GSE239282
- Alzheimer's disease: GSE125583, GSE150696, GSE153873, GSE159699, GSE161199, GSE162873, GSE173955, GSE181153, GSE184942, GSE193438, GSE203206, GSE231341, GSE236562, and GSE95673
- Parkinson disease: GSE148434, GSE172409, GSE202665, GSE205450, and GSE216281
- Depressive disorder: GSE185855
- Psoriasis: GSE136431 and GSE136434
- COVID-19: GSE178399
- Pulmonary fibrosis: GSE31934 and GSE99621
- IBD: GSE250063, GSE234981, GSE234736, GSE227747, GSE186295, GSE172372, GSE138364, GSE135223, GSE132732, GSE48634, GSE197698, GSE157020, GSE174159, GSE204868, GSE169568, GSE151686, GSE174460, GSE156044, GSE115390, GSE99816, GSE60083, GSE49702, and GSE26305
Removed/reprocessed datasets and comparisons
GSE71340 was moved to OncoHuman_B38 Land.
As part of our standard review process, comparisons and/or metadata for the following already-landed projects were revised and can be found by an updated OSModifiedDate “2024R2”.
Full project list
GSE100574, GSE107181, GSE111946, GSE115390, GSE118958, GSE119007, GSE121444, GSE122063, GSE124114, GSE125583, GSE129310, GSE129484, GSE131822, GSE132174, GSE132732, GSE132832, GSE135223, GSE138364, GSE143482, GSE144367, GSE148434, GSE150696, GSE151686, GSE153873, GSE154723, GSE156044, GSE157020, GSE157322, GSE157635, GSE158469, GSE159699, GSE161199, GSE162873, GSE169568, GSE172372, GSE172409, GSE173955, GSE174159, GSE174460, GSE17518, GSE178557, GSE181153, GSE182761, GSE184942, GSE185503, GSE185855, GSE186045, GSE186295, GSE189751, GSE190185, GSE193438, GSE197698, GSE202665, GSE202985, GSE203019, GSE203206, GSE204868, GSE205450, GSE205531, GSE207243, GSE210829, GSE216281, GSE227221, GSE227747, GSE228156, GSE231341, GSE234736, GSE234981, GSE235915, GSE236027, GSE236562, GSE238013, GSE239282, GSE250063, GSE26305, GSE31934, GSE38091, GSE40929, GSE48634, GSE49702, GSE54413, GSE60083, GSE60880, GSE6348, GSE7400, GSE95673, GSE9944, GSE99621, GSE99816, PRJNA369732
MouseDisease
This release adds 1138 samples and 476 comparisons from 22 datasets, including studies on:
- Alzheimer's disease: GSE140389, GSE168137, GSE168428, GSE168429, GSE168430, GSE169083, GSE174314, GSE181936, GSE197591, GSE221352, GSE222257, GSE166317, and GSE190186
- Age-related cognitive dysfunction: GSE213848
- Pulmonary fibrosis: GSE103355, GSE34814, GSE94522, and GSE98468
- Hippocampus sex differences: GSE184098
- Sperm energy restriction and recovery: GSE221741
Removed/reprocessed datasets and comparisons
GSE34818 and GPL13912 were removed and replaced by GSE34814.
As part of our standard review process, comparisons and/or metadata for the following already-landed projects were revised and can be found by an updated OSModifiedDate “2024R2”.
Full project list
GSE103355, GSE107180, GSE140389, GSE166317, GSE168137, GSE168428, GSE168429, GSE168430, GSE169083, GSE174314, GSE181936, GSE184098, GSE190186, GSE197591, GSE213848, GSE216163, GSE221352, GSE221741, GSE222257, GSE34814, GSE94522, GSE98468
RatDisease
This release adds 428 samples and 150 comparisons from 18 datasets, including studies on:
- Brain injury: GSE109902, GSE111452, GSE111452, GSE115067, GSE178564, GSE192979, GSE52763, GSE64978, GSE67836, GSE68207, GSE80174, and GSE80174
- Stroke: GSE149317, GSE199066, and GSE97537
- α-synucleinopathy: GSE246112
- Pulmonary hypertension: PRJNA637249
Removed/reprocessed datasets or comparisons:
No datasets were removed this release.
As part of our standard review process, comparisons and/or metadata for the following already-landed projects were revised
and can be found by an updated OSModifiedDate “2024R2”.
Full project list
GSE107180, GSE109902, GSE111452, GSE115067, GSE149317, GSE178564, GSE192979, GSE198756, GSE199066, GSE246112, GSE52763, GSE54413, GSE64978, GSE67836, GSE68207, GSE80174, GSE97537, PRJNA637249
Single Cell Land updates
This release adds 16 new tag-based datasets in HumanUMI and MouseUMI Lands, with 1.2 million cells, including 17 new cell type profiles and over 2000 comparisons, including HRA000425, GSE116106, GSE140393, GSE139555, GSE132257, GSE176465, GSE235923, GSE202052, GSE222647, GSE114396, GSE234933, GSE234817, GSE137398,
GSE220836, and GSE175649.
New profiled cell types include:
- Basal cell of submandibular gland — 2037 cells
- Duct epithelial cell — 3758 cells
- Endothelial cell of submandibular gland — 2913 cells
- Exocrine cell — 366 cells
- Intercalated duct cell of submandibular gland — 407 cells
- Mammary gland luminal hormone-responsive epithelial cell — 30,843 cells
- Mammary gland luminal secretory epithelial cell — 20,286 cells
- Mural cell — 1864 cells
- Myeloblast — 62,383 cells
- Neurogenic cell — 2098 cells
- Osteocyte — 527 cells
- Perivascular cell — 3113 cells
- Retinal amacrine and horizontal precursor cell — 1666 cells
- Seromucous acinar cell of submandibular gland — 1215 cells
- Striated duct cell of submandibular gland — 8202 cells
- Vascular leptomeningeal cell — 60 cells
ATCC Cell Line Land updates
ATCC Human summary
This release adds 147 samples to bring the total number of samples to 1751 from 364 unique cell lines.
Figure 4. Distribution of samples in ATCC_Human_B38_GC33 grouped by TissueCategory and colored by DiseaseCategory.
ATCC Mouse summary
The ATCC_Mouse_B38 Land added 22 new samples to bring the total number of samples to 220 from 52 unique cell lines.
Figure 5. Distribution of samples in ATCC_Mouse_B38 grouped by TissueCategory and colored by DiseaseCategory.
Highlighted topics
Quickly find cell lines that have been derived from the same parental cell line.
Figure 6. Heatmap displaying expression of CD14 and CD3E in cell lines derived from the parental JURKAT or THP1 cell lines. Upregulated genes are in red and downregulated genes are in blue.
Our journey through the ATCC Cell Lines continues. Next to be sequenced are cell lines related to the female reproductive
system.
Figure 7. Image of completed (green), in progress (light blue), and not started (dark blue) tissues available for mouse and human cell lines from ATCC.
Processing pipeline/curation protocol changes
Changes to curation protocol
Organism and Project.PlatformOrganism values converted from scientific name to common name as follows:
| Old value | New value |
|---|---|
| Homo sapiens | Human |
| Mus musculus | Mouse |
| Rattus norvegicus | Rat |
For instances where Organism contains multiple unsupported appended organisms due to multiple platforms (e.g., Influenza A virus; Macaca mulatta, Mustela putorius furo), the respective dataset corresponding organism is kept.Changes to processing pipelineAs part of the 2024R2 release, DESeq2R (v1.30) algorithm has replaced the previous OmicSoft implementation of DESeq2 for RatDisease_B6 and MouseDisease_B38 lands pipelines, to match the Human B38_GC33 lands. All RNA-seq comparisons were reprocessed with this new pipeline.