Additional file 1: Figures S1–16. of Single-cell transcriptome conservation in cryopreserved cells and tissues [stub]

Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Elisabetta Mereu, Maria Mendez-Lago, Diego Jaitin, Alberto Villanueva, August Vidal, Alex Martinez-Marti, Enriqueta Felip, Ana Vivancos, Hadas Keren-Shaul, Simon Heath (+4 others)
2017 Figshare  
Figure S1. Single cell transcriptome sequencing of 670 fresh and 816 cryopreserved cells using the MARS-Seq (a-c) and the Smart-seq2 (d, e) library preparation protocols. Samples included two human (HEK293 and K562), one mouse (NIH3T3) and one canine (MDCK) cell line, peripheral blood mononuclear cells (PBMC), a primary mouse colon sample and orthotopic tumor xenografts (patient-derived orthotopic xenograft, PDOX). Analyses were split by replicate experiments and conditions. Displayed are the
more » ... Displayed are the total number of reads per cell (a,d), the total number of detected genes per cell (b,e) and the number of detected transcripts (UMI counts) per cell (c). The results are displayed as boxplot indicating median values (black bar) per experiment and condition. Figure S2. (a-d) Cumulative gene counts split by fresh (red) or cryopreserved (blue) cells and analyzed using randomly sampled cells (average of 100 permutations). Displayed are results for K562 (experiment 1, a), HEK293 (experiment 1, b), NIH3T3 (c) and MDCK (d) cell lines. Figure S3. Distribution of sequencing reads numbers per single cell split by conditions (fresh (red); cryopreserved -80ºC: blue; cryopreserved liquid nitrogen: green). Displayed are the distributions for all MARS-Seq experiments (a-h) indicating the median number of reads per single cell (horizontal lines). Experiment types are indicated. Figure S4. MARS-Seq library complexity assessment of fresh (red) or cryopreserved (blue) cells using the number of uniquely detected transcripts. (a-d) Comparative analysis of the number of sequencing reads and detected transcripts using a linear model. The slope of the regression line was calculated separately for fresh and cryopreserved cells. Displayed are results for K562 (experiment 1, a), HEK293 (experiment 1, b), NIH3T3 (c) and MDCK (d) cell lines. Figure S5. MARS-Seq library complexity assessment of fresh (red) or cryopreserved (blue) cells using the total number of detected genes. (a-d) Comparative analysis of the number of sequencing reads and detected tran [...]
doi:10.6084/m9.figshare.c.3706726_d1.v1 fatcat:3cfd42cliremhnyqqll5wp35x4