OMIX001042

1Summary
Title Parallel version of hECA data with batch-correction
Description Considering some users may prefer to be able to download data that have been processed with more batch-correction processing, we did a series of comparison experiments on the popular methods, and chose to use the Harmony method (Korsunsky et al., 2019). Harmony is one of the most used integration methods but it does not provide the corrected matrix. We added an extra step upon the standard Harmony method to calculate the corrected expression matrix from the vectors in the corrected embedding space with the inverse-transformation. We had experimented with multiple methods for cross-organ batch-effect correction but none of them worked well since there are no shared cell types across some organs. Therefore, we applied the extended Harmony method on cells of the same organ, and do this batch-effect correction separately for each organ. We provided the data thus processed as a parallel version of the hECA data for each organ here.
Organism Homo
Data Type Mixed
Data Accessibility Open-access
BioProject PRJCA008680
Release Date 2022-03-17
Submitter Yixin Chen (ysionchen@gmail.com)
Organization Tsinghua University
Submission Date 2022-03-16
2Files & Download

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File ID File Title Number/Samples File Type File Size File Suffix Download
OMIX001042-20-01 Ilem dataset with batch-correction in hECA v1.0 1 Transcriptomic 296.01 MB rds
OMIX001042-20-02 Adipose dataset with batch-correction in hECA v1.0 1 Transcriptomic 265.01 MB rds
OMIX001042-20-03 Adrenal gland dataset with batch-correction in hECA v1.0 1 Transcriptomic 3.72 GB rds
OMIX001042-20-04 Bladder dataset with batch-correction in hECA v1.0 1 Transcriptomic 160.92 MB rds
OMIX001042-20-05 Adult blood dataset with batch-correction in hECA v1.0 1 Transcriptomic 1.38 GB rds
OMIX001042-20-06 Fetal blood dataset with batch-correction in hECA v1.0 1 Transcriptomic 2.12 GB rds
OMIX001042-20-07 Bone marrow dataset with batch-correction in hECA v1.0 1 Transcriptomic 1.09 GB rds
OMIX001042-20-08 Adult brain dataset with batch-correction in hECA v1.0 1 Transcriptomic 3.39 GB rds
OMIX001042-20-09 Fetal brain dataset with batch-correction in hECA v1.0 1 Transcriptomic 9.34 GB rds
OMIX001042-20-10 Bronchi dataset with batch-correction in hECA v1.0 1 Transcriptomic 2.15 GB rds
OMIX001042-20-11 Colon dataset with batch-correction in hECA v1.0 1 Transcriptomic 3.27 GB rds
OMIX001042-20-12 Duodenum dataset with batch-correction in hECA v1.0 1 Transcriptomic 331.28 MB rds
OMIX001042-20-13 Adult eye dataset with batch-correction in hECA v1.0 1 Transcriptomic 7.33 GB rds
OMIX001042-20-14 Fetal eye dataset with batch-correction in hECA v1.0 1 Transcriptomic 2.32 MB rds
OMIX001042-20-15 Gallbladder dataset with batch-correction in hECA v1.0 1 Transcriptomic 2.07 GB rds
OMIX001042-20-16 Adult heart dataset with batch-correction in hECA v1.0 1 Transcriptomic 43.89 GB rds
OMIX001042-20-17 Fetal heart dataset with batch-correction in hECA v1.0 1 Transcriptomic 2.78 GB rds
OMIX001042-20-18 Adult Intestine dataset with batch-correction in hECA v1.0 1 Transcriptomic 2.63 GB rds
OMIX001042-20-19 Fetal Intestine dataset with batch-correction in hECA v1.0 1 Transcriptomic 2.68 GB rds
OMIX001042-20-20 Jejunum dataset with batch-correction in hECA v1.0 1 Transcriptomic 562.96 MB rds
OMIX001042-20-21 Adult kidney dataset with batch-correction in hECA v1.0 1 Transcriptomic 3.85 GB rds
OMIX001042-20-22 Fetal kidney dataset with batch-correction in hECA v1.0 1 Transcriptomic 3.47 GB rds
OMIX001042-20-23 Liver dataset with batch-correction in hECA v1.0 1 Transcriptomic 8.08 GB rds
OMIX001042-20-24 Adult lung dataset with batch-correction in hECA v1.0 1 Transcriptomic 541.76 MB rds
OMIX001042-20-25 Fetal lung dataset with batch-correction in hECA v1.0 1 Transcriptomic 32.38 MB rds
OMIX001042-20-26 Oesophagus dataset with batch-correction in hECA v1.0 1 Transcriptomic 13.54 GB rds
OMIX001042-20-27 Ovary dataset with batch-correction in hECA v1.0 1 Transcriptomic 906.96 MB rds
OMIX001042-20-28 Fetal pancreas dataset with batch-correction in hECA v1.0 1 Transcriptomic 2.42 GB rds
OMIX001042-20-29 Plancenta dataset with batch-correction in hECA v1.0 1 Transcriptomic 2.41 GB rds
OMIX001042-20-30 Pleura dataset with batch-correction in hECA v1.0 1 Transcriptomic 6.05 GB rds
OMIX001042-20-31 Rectum dataset with batch-correction in hECA v1.0 1 Transcriptomic 1.06 GB rds
OMIX001042-20-32 Rib dataset with batch-correction in hECA v1.0 1 Transcriptomic 1.31 GB rds
OMIX001042-20-33 Skin dataset with batch-correction in hECA v1.0 1 Transcriptomic 853.2 MB rds
OMIX001042-20-34 Spinal cord dataset with batch-correction in hECA v1.0 1 Transcriptomic 1.06 GB rds
OMIX001042-20-35 Spleen dataset with batch-correction in hECA v1.0 1 Transcriptomic 3.82 GB rds
OMIX001042-20-36 Adult stomach dataset with batch-correction in hECA v1.0 1 Transcriptomic 2.12 GB rds
OMIX001042-20-37 Fetal stomach dataset with batch-correction in hECA v1.0 1 Transcriptomic 1.09 GB rds
OMIX001042-20-38 Testis dataset with batch-correction in hECA v1.0 1 Transcriptomic 1.86 GB rds
OMIX001042-20-39 Thymus dataset with batch-correction in hECA v1.0 1 Transcriptomic 517.34 MB rds
OMIX001042-20-40 Thyroid dataset with batch-correction in hECA v1.0 1 Transcriptomic 3.29 GB rds
OMIX001042-20-41 Ureter dataset with batch-correction in hECA v1.0 1 Transcriptomic 125.3 MB rds
OMIX001042-20-42 Vessel dataset with batch-correction in hECA v1.0 1 Transcriptomic 2.81 GB rds
3Relevant Publications
Paper Title Journal Name Publish Time Accession Citing Type
hECA: The cell-centric assembly of a cell atlas iScience 2022-05 OMIX001042 Deposit

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