Journal: bioRxiv

Article Title: PySeq2500: An open source toolkit for repurposing HiSeq 2500 sequencing systems as versatile fluidics and imaging platforms

doi: 10.1101/2021.08.27.457864

Figure Lengend Snippet: High-plex 4i tissue profiling of human postmortem spinal cord. Fresh frozen tissue sections from ALS patient spinal cords were subjected to 14-plex profiling over six 4i cycles. (A) K-means clustering of 4i data was used to visualize tissue domains defined by all 14 channels across the entire tissue section. Each of 7 clusters is assigned a unique color and inset locations are noted (B-E). (B’) Higher magnification image of anterior horn inset region B. Cell type marker MBP (cyan) is expressed by oligodendrocytes, MAP2 (magenta) is expressed in neurons and neuronal processes, and ELAVL3 (yellow) is expressed by neurons, including motor neurons. (B’’) Same as B’, but yellow is used to visualize tissue autofluorescence. (B’’’) Pathological markers P62 (cyan), TDP-43 (magenta), and hyperphosphorylated TDP43 (yellow) are visualized in the same FOV as in B’ and B’’. (C) Higher magnification image of lateral white matter inset region C. Cell type markers NFH expressed in neurons (cyan), GFAP expressed in astrocytes (magenta), and CD68 expressed in activated microglia (yellow) are visualized. (D) Higher magnification image of lateral white matter inset region D. Cell type markers NFH expressed in neurons (cyan), IBA1 expressed in microglia (yellow), and nuclear envelope marker LMNB1 (magenta), are visualized. (E) Higher magnification image of dorsal horn inset region E. Cell type markers CD34 expressed in endothelial cells (cyan), ALDH1L1 expressed in astrocytes (yellow), and nuclear envelope marker LMNB1 (magenta), are visualized.

Article Snippet: Human spinal cord 4i data was generated over six cycles using CD34 (R&D Systems, AF7227), LMNB1 (Sigma, AMAB91251), CD68 (DAKO, M0814), TDP-43 (Proteintech, 10782-2-AP), MAP2 (Abcam, ab5392), ELAVL3 (Invitrogen, A-21271), pTDP-43 (Proteintech, 22309-1-AP), NFH (Abcam, ab4680), IBA1 (Abcam, ab178847), GFAP (Abcam, ab4647), MBP (Atlas, AMAb91062), ALDH1L1 (Atlas, HPA050139), and P62 (Abcam, ab56416) antibodies.

Techniques: Marker

Journal: Oncotarget

Article Title: Stabilin-1 is expressed in human breast cancer and supports tumor growth in mammary adenocarcinoma mouse model

doi: 10.18632/oncotarget.8857

Figure Lengend Snippet: Immunofluorescent staining for co-expression of stabilin-1 with other cellular markers was performed on human breast cancer biopsies and analysed by confocal microscopy. Panel A. shows the area with low stabilin-1 expression on CD68high TAM; panel B. shows region with stabilin-1 expression on CD68low/negative cells; panel C. shows co-expression of stabilin-1 on CD68+ TAM; panel D. demonstrates the area with heterogeneous CD68 and stabilin-1 expression. Co-expression of stabilin-1, CD68, and CD163 is shown on panel E. yellow arrow indicates stabilin-1+CD163+CD68+ triple positive cell, white arrow indicates stabilin-1+CD163-CD68- cell; co-expression of stabilin-1 with CD34, CD31 and pan-cytokeratin is shown on panels F , G and H. respectively.

Article Snippet: Following primary anti-human antibodies were used: mouse CD68 (Zytomed), goat SPARC, clone AF941, goat CD163, sheep CD34 (all from R&D systems), rabbit anti-stabilin-1, clone RS1 (self-produced), mouse CD31 (DAKO), and mouse pan-cytokeratin (DAKO, clone AE1/AE3).

Techniques: Staining, Expressing, Confocal Microscopy

Journal: Nucleic Acids Research

Article Title: Mitogen-induced recruitment of ERK and MSK to SRE promoter complexes by ternary complex factor Elk-1

doi: 10.1093/nar/gkn099

Figure Lengend Snippet: Pre-initiation complexes on SRE promoters contain ERKs and MSK1. ( a ) Nuclear extracts from unstimulated (lanes 1–7) or serum-stimulated (lanes 8–14) cells were used for PIC assembly on SRE (lanes 2 and 9), DSE (lanes 3 and 10) or TATA (lanes 4 and 11) templates. Complexes were isolated, washed and resolved by SDS–PAGE for analysis by immunoblotting with antibodies against ERKs (upper panel), phospho-ERKs, JNKs and p38 (lower). Inputs were resolved in lanes 1 and 8; flow through fractions in lanes 5–7 and 12–14. ( b ) As in (a) except with antibodies against MSK1 (upper panel) and RSK2 (lower panel).

Article Snippet: Antibodies used were as follows: the ElkC and JNK/SAPK are rabbit polyclonal antibodies raised against recombinant proteins; the SRF (H-300), ERK1/ERK2 goat (C-14), MSK1 (H-65), RSK2 mouse monoclonal (E-1), TBP (N-12), p300 (C-20), RAP74 (C-18), MED1 (C-19), Elk-1 (I-20) and p Elk-1 mouse monoclonal (B-4) were from Santa Cruz; the MSK1 sheep polyclonal (for immunoblots) and HDAC1 (2E10) and HDAC2 (3F3) mouse monoclonals and phospho/acetyl-H3S10K14 rabbit polyclonal were from Upstate; the p ERK rabbit monoclonal (20G11) and p38 (9212) were from Cell Signaling; the MED23 mouse monoclonal (D27) was from BD Biosciences; the RNAPII p S5-CTD (H14), p S2-CTD (H5) and RNAPII-CTD (8WG16) mouse monoclonals were from Abcam; the AlexaFluor 488 goat anti-mouse/AlexaFluor 568 goat anti-rabbit were from Invitrogen, Molecular Probes.

Techniques: Isolation, SDS Page, Western Blot