Publication data

1	Antibody Response Data. Results from 12634 immunizations using different Protein Epitope Signature Tags (PrEST) as antigens to generate monospecific antibodies. The result is given as amount (mg) specific antibody obtained after immunization and affinity purification using the same specific protein fragment (PrEST) as antigen and purification partner. The comma-separated file includes: antigen id, antibody id, antigen sequence and antibody amount (mg).	Related to publication: Rockberg J, Uhlén M. Prediction of antibody response using recombinant human protein fragments as antigen. Protein Sci. 2009 18(11):2346-55.	antibodyresponse.csv.zip CSV-file, 927.7 KB

2	TMA expression data. Expression profiles for proteins based on immunohistochemisty using tissue micro arrays. The comma-separated file includes antibody identifier (hpa_id), Ensembl gene identifier (ensembl_gene_id), tissue name, intensity, fraction and the summary expression value. The data is based on The Human Protein Atlas version 4.1 and Ensembl version 54.36.	Related to publication: Pontén F, Gry M, Fagerberg L, Lundberg E, Asplund A, Berglund L, Oksvold P, Björling E, Hober S, Kampf C, Navani S, Nilsson P, Ottosson J, Persson A, Wernérus H, Wester K, Uhlén M. A global view of protein expression in human cells, tissues, and organs. Mol Syst Biol. 2009 5:337.	expression_data.TMA.csv.zip CSV-file, 1.7 MB

3	CMA expression data. Expression profiles for proteins based on immunohistochemisty using cell micro arrays. The comma-separated file includes antibody identifier (hpa_id), Ensembl gene identifier (ensembl_gene_id), name of cell line (celline) and the summary expression value in that cell line (summary_expression_value). The data is based on The Human Protein Atlas version 4.1 and Ensembl version 54.36.	Related to publication: Pontén F, Gry M, Fagerberg L, Lundberg E, Asplund A, Berglund L, Oksvold P, Björling E, Hober S, Kampf C, Navani S, Nilsson P, Ottosson J, Persson A, Wernérus H, Wester K, Uhlén M. A global view of protein expression in human cells, tissues, and organs. Mol Syst Biol. 2009 5:337.	expression_data.CMA.csv.zip CSV-file, 892.2 KB

4	IF expression data. Expression profiles for proteins based on immunofluorescently stained cells. The comma-separated file includes antibody identifier (hpa_id), Ensembl gene identifier (ensembl_gene_id), name of cell line (celline) and the summary expression value in that cell line (summary_expression_value). The data is based on The Human Protein Atlas version 4.1 and Ensembl version 54.36.	Related to publication: Pontén F, Gry M, Fagerberg L, Lundberg E, Asplund A, Berglund L, Oksvold P, Björling E, Hober S, Kampf C, Navani S, Nilsson P, Ottosson J, Persson A, Wernérus H, Wester K, Uhlén M. A global view of protein expression in human cells, tissues, and organs. Mol Syst Biol. 2009 5:337.	expression_data.IF.csv.zip CSV-file, 32.5 KB

5	RNA isoform data RNA levels in 32 tissues based on RNA-seq. The tab-separated file includes Ensembl gene identifier ("Gene"), Ensembl transcript identifier ("Transcript"), analysed sample ("Sample") and fragments per kilobase of transcript per million fragments mapped ("FPKM"). The data is based on The Human Protein Atlas version version 13 and Ensembl version 75.37.	Related to publication: Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CA, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist PH, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, von Feilitzen K, Forsberg M, Persson L, Johansson F, Zwahlen M, von Heijne G, Nielsen J, Pontén F. Tissue-based map of the human proteome. Science 2015 347(6220):1260419.	rna_transcript.tsv.gz TSV-file, 56.3 MB

6	Integrated correlation network. Integrated multiomic correlation network including clinical chemistry, proteomics, transcriptomics, lipidomics, metabolomics, immune cytome, autoantibodies as well as gut microbiota composition. The tab-separated txt file includes: node ids, rho spearman correlation and adjusted p-values.	Related to publication: Tebani A, Gummesson A, Zhong W, Koistinen IS, Lakshmikanth T, Olsson LM, Boulund F, Neiman M, Stenlund H, Hellström C, Karlsson MJ, Arif M, Dodig-Crnković T, Mardinoglu A, Lee S, Zhang C, Chen Y, Olin A, Mikes J, Danielsson H, von Feilitzen K, Jansson PA, Angerås O, Huss M, Kjellqvist S, Odeberg J, Edfors F, Tremaroli V, Forsström B, Schwenk JM, Nilsson P, Moritz T, Bäckhed F, Engstrand L, Brodin P, Bergström G, Uhlen M, Fagerberg L. Integration of molecular profiles in a longitudinal wellness profiling cohort. Nat Commun. 2020 11(1):4487.	scapis_wellness_correlation_network_all_data.txt.gz TSV-file, 725.8 MB

7	FACS sorting of FUCCI U-2 OS cells for scRNA-seq In preparation for scRNA-seq of cells in different phases of the cell cycle, a total of 1,152 cells were sorted by FACS into three 384-well plates using a BD Influx System (BD Biosciences, San Jose, CA). Singlet cells were targeted using the forward scattering width. Approximately equal numbers of cells in G1 (red), S (yellow), and G2 (green) phases were selected based on their fluorescence intensity of GFP-tagged GMNN (530 nm) and RFP-tagged CDT1 (585 nm). The comma-separated files include the recorded mean fluorescence intensities for GFP-tagged GMNN (530/40 [488]) and RFP-tagged CDT1 (585/29 [561]) in each well, as well as the identification of objects in the well as singlet cells (Singlets) in the G1, S (S-ph) or G2/M (G2M) phases of the cell cycle. scRNA-seq of FUCCI U-2 OS A total of 1,152 single U2OS FUCCI cells were sorted by FACS, and RNA-Seq was collected for each cell using the SMART-seq2 extraction and library preparation protocol on an Illumina HiSeq 2000 sequencer. FASTQ files containing 725 reads are available at GEO with accession GSE146773.	Related to publication: Mahdessian D, Cesnik AJ, Gnann C, Danielsson F, Stenström L, Arif M, Zhang C, Le T, Johansson F, Shutten R, Bäckström A, Axelsson U, Thul P, Cho NH, Carja O, Uhlén M, Mardinoglu A, Stadler C, Lindskog C, Ayoglu B, Leonetti MD, Pontén F, Sullivan DP, Lundberg E. Spatiotemporal dissection of the cell cycle with single-cell proteogenomics. Nature. 2021 590(7847):649-654.	pubmed33627808_FUCCI-FACS-data.zip CSV-files, 28.4 KB