frozen acc  (GE Healthcare)

Journal: Diagnostic Pathology

Article Title: A comparative proteomic study identified calreticulin and prohibitin up-regulated in adrenocortical carcinomas

doi: 10.1186/1746-1596-8-58

Figure Lengend Snippet: Representative images of immunohistochemical results. Expression of calreticulin, prohibitin and HSP60 in adrenocortical carcinomas (ACC), adrenocortical adenomas (ACA) and normal tissues (N) ( A ). Calreticulin and prohibitin but not HSP60 were overexpressed in ACC compared with adrenocortical adenomas (ACA) and normal tissues ( B ).

Article Snippet: Frozen ACC and normal adjacent adrenocortical tissues were first homogenized using a sample grinding kit (GE Healthcare) with a lysis buffer (7 M urea, thiourea 2 M, 2% CHAPS, 18 mM DTT, 1 mM PMSF, 0.5% IPG buffer pH3~10NL), and then the extracts were centrifuged at 12,000 g, 4°C, for 1 hr.

Techniques: Immunohistochemical staining, Expressing

Journal: bioRxiv

Article Title: Integration of an anellovirus genome in the SKNO-1 acute myeloid leukemia cell line

doi: 10.64898/2026.01.22.701047

Figure Lengend Snippet: A) Venn diagram illustrating the overlap between human cell line SRA datasets and those containing anellovirus k-mers. B) Correlation analysis of SRA datasets with anellovirus k-mers hits, categorized by hit frequency: low (2-9 k-mers), medium (10-100 k-mers) and high (>100 k-mers). The dotted line connects each dataset to its corresponding number of hits. C) Classification of anellovirus k-mer-enriched SRA datasets by human cell line type. D) Overview of sequencing methodology for anellovirus k-mer-rich SKNO-1 SRA datasets.

Article Snippet: Frozen SKNO-1 cell pellets (5 x 10 6 cells each) from the DSMZ and JCRB were submitted to the Translational Genomics Research Institute (TGen) for high-molecular-weight DNA extraction using the NEB Monarch HMW Extraction Kit for Cells & Blood.

Techniques: Sequencing

Journal: bioRxiv

Article Title: Integration of an anellovirus genome in the SKNO-1 acute myeloid leukemia cell line

doi: 10.64898/2026.01.22.701047

Figure Lengend Snippet:

Article Snippet: Frozen SKNO-1 cell pellets (5 x 10 6 cells each) from the DSMZ and JCRB were submitted to the Translational Genomics Research Institute (TGen) for high-molecular-weight DNA extraction using the NEB Monarch HMW Extraction Kit for Cells & Blood.

Techniques:

Journal: bioRxiv

Article Title: Integration of an anellovirus genome in the SKNO-1 acute myeloid leukemia cell line

doi: 10.64898/2026.01.22.701047

Figure Lengend Snippet: A) Schematic representation of chromosome 21 in the SKNO-1 cell line, showing the integration site of the anellovirus genome (dotted green line). Red represents the centromere, blue indicates the repetitive region, and the grayscale sharing indicates Giemsa bands (darker shades correspond to higher heterochromatin and greater AT-rich regions). B) Detailed schematic of anellovirus integration within chromosome 21. The pink region denotes the anellovirus genome, with arrows indicating open reading frames (ORF). A grey arrow highlights ORF2 containing an early stop codon at position codon position 2, while an asterisk (*) marks the truncation of ORF1, preventing overlap with ORF3. The violet line highlights the duplicated sequences located at both termini of the viral genome, which differ by two-point mutations (C→A and G→A), while the blue region indicates an additional nucleotide segment corresponding to a MaLR-like element. C) Comparison between wild-type chromosome 12 and the chromosome 21 with the anellovirus genome integration. The integrant interrupts the RNA45SN2/RNA28SN2 rRNA gene. Dotted green lines indicate the region that has been altered within chromosome 21 including specific coordinates for the integration site. Below the schematic of chromosome 21 with the integration, PacBio long reads are shown (represented by grey rectangles), confirming the presence of the integrant in the SKNO-1 J subline cell.

Article Snippet: Frozen SKNO-1 cell pellets (5 x 10 6 cells each) from the DSMZ and JCRB were submitted to the Translational Genomics Research Institute (TGen) for high-molecular-weight DNA extraction using the NEB Monarch HMW Extraction Kit for Cells & Blood.

Techniques: Comparison

Journal: bioRxiv

Article Title: Integration of an anellovirus genome in the SKNO-1 acute myeloid leukemia cell line

doi: 10.64898/2026.01.22.701047

Figure Lengend Snippet: Reads from ChIP-Seq SRA datasets were trimmed with fastp and aligned to a de-novo assembly of the anellovirus genome constructed from RNA-Seq data of the SKNO-1 cell line (see Methods). Alignment depth is plotted across the 3,425 bp reference genome. Plots are labeled with the associated SRA and ChIP-Seq experimental conditions (e.g. protein targeted, buffer). Predicted open reading frame coordinate intervals of the anellovirus assembly are displayed at the bottom. The span of the entire assembly is depicted by the black bar, and ORFs are shown as yellow boxes.

Article Snippet: Frozen SKNO-1 cell pellets (5 x 10 6 cells each) from the DSMZ and JCRB were submitted to the Translational Genomics Research Institute (TGen) for high-molecular-weight DNA extraction using the NEB Monarch HMW Extraction Kit for Cells & Blood.

Techniques: ChIP-sequencing, Construct, RNA Sequencing, Labeling

Journal: bioRxiv

Article Title: Integration of an anellovirus genome in the SKNO-1 acute myeloid leukemia cell line

doi: 10.64898/2026.01.22.701047

Figure Lengend Snippet: A) Maximum-likelihood phylogenetic tree of ORF1 nucleotide sequences from Alphatorquevirus, Betatorquevirus, and Gammatorquevirus reference genomes. Ultrafast bootstrap support values (1,000 replicates) are shown for key nodes. Anellovirus assembled from the SKNO-1 cell line is highlighted in red, and branches corresponding to the clade containing this virus together with sequences retrieved from NCBI BLAST showing >90% genomic identity are shown in pink. The Betatorquevirus clade is collapsed and represented as a green triangle, while the Gammatorquevirus clade is collapsed in blue. Branch lengths correspond to the number of substitutions per site. B) P-distance matrix comparing the SKNO-1 anellovirus, the SKNO-1–like anellovirus clade, and representative sequences of Alphatorquevirus homin27, homin28, and homin29. Bootstrap standard errors (100 replicates) are shown in italics.

Article Snippet: Frozen SKNO-1 cell pellets (5 x 10 6 cells each) from the DSMZ and JCRB were submitted to the Translational Genomics Research Institute (TGen) for high-molecular-weight DNA extraction using the NEB Monarch HMW Extraction Kit for Cells & Blood.

Techniques: Virus

Journal: bioRxiv

Article Title: Integration of an anellovirus genome in the SKNO-1 acute myeloid leukemia cell line

doi: 10.64898/2026.01.22.701047

Figure Lengend Snippet: A) Multiple alignment of amino acid sequence between Betatorquevirus LY1 ORF1 and Alphatorquevirus sp. isolate SKNO-1 ORF1 starting with ATG or ACG. The identical sites are marked as black. Betatorquevirus LY1 ORF1 is annotated with purple bar, and Alphatorquevirus sp. isolate SKNO-1 ORF1 is annotated with orange and yellow bar. B) The PDB structures of Betatorquevirus LY1 ORF1 and AlphaFold predicted structure Alphatorquevirus sp. isolate SKNO-1 ORF1 starting with ATG or ACG. The motif ARM, P2, P1, JR, and C-terminal are marked on the structure. Pentamers structures are shown on the right.

Article Snippet: Frozen SKNO-1 cell pellets (5 x 10 6 cells each) from the DSMZ and JCRB were submitted to the Translational Genomics Research Institute (TGen) for high-molecular-weight DNA extraction using the NEB Monarch HMW Extraction Kit for Cells & Blood.

Techniques: Sequencing