Journal: Science immunology

Article Title: Human Innate Lymphoid Cell Precursors Express CD48 that Modulates ILC Differentiation through 2B4 Signaling

doi: 10.1126/sciimmunol.aay4218

Figure Lengend Snippet: (A) Freshly isolated UCB-derived CD34+ HSCs were stained for CD244 and CD48 (representative, n=4). (B) CD244 in CD34+CD48− cells (aqua) and in CD34+CD48+ cells (red) for day 1 and day 3 UCB-derived CD34+ HSCs (representative, n=4). (C) SAP mRNA expression in day 5 CD34+CD48− and CD34+CD48+ cells (n=4/group). (D and E) Anti-CD244 and anti-CD48 blocking antibodies or isotype IgG controls? were added to differentiating CD34+α4β7+CD48+ cultures to block CD244 signaling. (F and G) CD34+α4β7+CD48+ cells were plated on anti-CD244 or IgG coated plates twice for 4 days prior to 21 days of differentiation to activate CD244 signaling via cross-linking. Cells were stained for ILCs, and the percentage (D and F) or absolute number (E and G) of CD94+ NK cells, CD294+ ILC2 and CD117+ ILC3 are shown (n=4/group). (H) CD244+ cultures are shown for cells transfected with control or CD244 gRNA (n=3/group). (I) Representative ILC2 (CD294) staining for cultures transfected with control or CD244 gRNA. (J) Dot plot showing generation of ILC2s from cultures that express (control gRNA) or lack (CD244 gRNA) CD244. (C-H) Mean ± SD, paired t-tests (C, F, G and H) or one-way ANOVA (D and E) and p-values are depicted.

Article Snippet: The Alt-R Cas9 Nuclease V3, universal tracrRNA, CD244 gRNA and non-human control gRNA were purchased from Integrated DNA Technologies.

Techniques: Isolation, Derivative Assay, Staining, Expressing, Blocking Assay, Transfection

Journal: Oncotarget

Article Title: LINE-1 hypomethylation in normal colon mucosa is associated with poor survival in Chinese patients with sporadic colon cancer

doi:

Figure Lengend Snippet: Bisulfite-treated DNA samples from adjacent normal mucosa were subjected to PCR amplification and were quantitatively analyzed by pyrosequencing. The C base marked in yellow served as a quality control of the bisulfite conversion efficiency. Four analyzed CpG sites are highlighted in blue, and the percent methylation rate is provided for each site. The mean percentage was computed as the LINE-1 methylation rate (LMR) for each case. Two cases with relatively higher (73.8%, A. ) or lower (19.4%, B. ) LMR were shown, respectively.

Article Snippet: In this system, a bisulfite-converted universal human DNA standard of 100% methylation (#D5015, ZYMO Research, USA) and ALU-C4 were used as the reference template and internal control, respectively.

Techniques: Amplification, Methylation

Journal: bioRxiv

Article Title: NASTRA: Innovative Short Tandem Repeat Analysis through Cluster-Based Structure-Aware Algorithm in Nanopore Sequencing Data

doi: 10.1101/2023.11.04.565630

Figure Lengend Snippet: Overview of the study design. a Nanopore sequencing were conducted on collected 84 individual samples (88 DNA samples) with different amplification methods and flow cells. With ForenSeq data and PowerSeq data, we optimized the parameters of NASTRA, and conduted performance evalutation and real-time scenario tesing. b. The workflow of NASTRA: 1. Extracing aligned reads from bam file; 2. Flanking regions of each read are trimmed; 3. Reads clustering are performed to find candidate allele sequences; 4. Repeat structure of each allele is inferred by the recursive inference algorithm; 5. Genotype calling.

Article Snippet: In order to perform a real-time scenario tesing, we collected 8 control DNA samples including 3 forensic DNA controls (2800M from Promega, 9947A and 9948 from Origene), and 5 cell line standards (NA12878, NA24143, NA24149, NA24694, and NA24695 from Coriell Institute).

Techniques: Nanopore Sequencing, Amplification

Journal: bioRxiv

Article Title: NASTRA: Innovative Short Tandem Repeat Analysis through Cluster-Based Structure-Aware Algorithm in Nanopore Sequencing Data

doi: 10.1101/2023.11.04.565630

Figure Lengend Snippet: Performance on real-time scenario tesing. a. overview of genotyping results obtained from 8 DNA standard samples across 27 autosomal STRs, with variations in sequencing durations, using a R9.4.1 flow cell. b. The percentages of genotyping results achieving exact match, incomplete match or imbalance/interpretation across all 8 samples, with different sequencing durations. c. The distribution of sequencing depth in relation to different sequencing durations.

Article Snippet: In order to perform a real-time scenario tesing, we collected 8 control DNA samples including 3 forensic DNA controls (2800M from Promega, 9947A and 9948 from Origene), and 5 cell line standards (NA12878, NA24143, NA24149, NA24694, and NA24695 from Coriell Institute).

Techniques: Sequencing