Journal: bioRxiv

Article Title: Characterization of human-iPSCs derived spinal motor neurons by single-cell RNA sequencing

doi: 10.1101/2019.12.28.889972

Figure Lengend Snippet: (A-B) Representative images (A) and quantification (B) of neural progenitor cells (NPCs) subjected to immunocytochemistry with either anti-SOX1 or anti-HOXC4 antibodies 6 days after the start of the induction protocol. (C-D) Representative images (C) and quantification (D) of MNPCs subjected to immunocytochemistry with either anti-OLIG2 or anti-PAX6 antibodies 12 days after the start of the induction protocol. (E-F) Representative images (E) and quantification (F) of V3 interneuron progenitors (INPs) subjected to immunocytochemistry with anti-NKX2.2 antibody or V2 INPs visualized with anti-CHX10 antibody, 12 days after the start of the induction protocol. For all graphs, n = 3 cultures (with >500 cells in random fields for each culture). Scale bars, 50 μm.

Article Snippet: The following primary antibodies were used: mouse anti-OLIG2 (1/100; Millipore Corp.; Billerica, MA, USA; Cat. No. MABN50); rabbit anti-PAX6 (1/500; Covance; Emeryville, CA, USA; Cat. No. PRB-278P); rabbit anti-HOMEOBOX C4 (HOXC4) (1/150; kindly provided by Dr. Jeremy Dasen, New York University School of Medicine); goat anti-SRY-BOX 1 (SOX1) (1/500; R&D Systems; Cat. No. AF3369; mouse anti-NK2 HOMEOBOX 2 (NKX2.2) (1/100; DSHB; Cat. No. 74.5A5-c); rabbit anti-HOMEOBOX PROTEIN CHX10 (CHX10) (1/10,000; kindly provided by the late Dr. Thomas Jessell, Columbia University); mouse anti-HOMEOBOX PROTEIN HB9 (HB9) (1/30; DSHB; Cat. No. 81.5C10-c); mouse anti-ISLET1 (ISL1) (1/30; DSHB; Cat. No. 39.4D5-c); rabbit anti-LIMB HOMEOBOX CONTAINING 3 (LHX3) (1/100; Abcam; Toronto, ON, Canada; Cat. No. ab14555), goat anti-FORKHEAD BOX PROTEIN 1 (FOXP1) (1/100; R&D Systems; Cat. No. AF4534), and guinea pig anti-SCIP (1/16,000; kindly provided by Dr. Jeremy Dasen).

Techniques: Immunocytochemistry

Journal: bioRxiv

Article Title: Characterization of human-iPSCs derived spinal motor neurons by single-cell RNA sequencing

doi: 10.1101/2019.12.28.889972

Figure Lengend Snippet: (A) t-SNE plot of h-iPSC derived MN culture after 28 days of differentiation, showing 14 cell shared nearest neighbour graph-based cell clusters. (B) Percentage of total cells present in each cluster. (C) Relative proportion of iPSCs, NPCs, INs, MNs and glial cells, identified based on the specific expression of the following genes: NANOG and OCT4 for iPSCs; SOX1, SOX2 , and MKI67 for NPCs; PAX2, PAX3, LBX1, EVX1, EN1, CHX10, GATA3, SOX14, SIM1, TLX3 for INs; OLIG2, NEUROG2, HB9, ISL1, ISL2, CHAT for MNs; S100B, SOX9 for glial cells. (D) t-SNE plot colored for MNPCs and MNs (orange dots), identified based on the specific expression of the following genes: NEUROG2, HB9, ISL1, ISL2, CHAT . Blue dots represent the rest of the cells. (E) Proportion of each of the spinal interneuron (IN) subtypes identified based on combinatorial gene expression patterns: dorsal INs (dINs), LBX1, PAX2, TLX3 ; V0, EVX1 + / EN1 - ; V1, EVX1 - / EN1 + ; (V2), CHX10, SOX14, GATA3 ; (V3) SIM1, NKX2 . 2 .

Article Snippet: The following primary antibodies were used: mouse anti-OLIG2 (1/100; Millipore Corp.; Billerica, MA, USA; Cat. No. MABN50); rabbit anti-PAX6 (1/500; Covance; Emeryville, CA, USA; Cat. No. PRB-278P); rabbit anti-HOMEOBOX C4 (HOXC4) (1/150; kindly provided by Dr. Jeremy Dasen, New York University School of Medicine); goat anti-SRY-BOX 1 (SOX1) (1/500; R&D Systems; Cat. No. AF3369; mouse anti-NK2 HOMEOBOX 2 (NKX2.2) (1/100; DSHB; Cat. No. 74.5A5-c); rabbit anti-HOMEOBOX PROTEIN CHX10 (CHX10) (1/10,000; kindly provided by the late Dr. Thomas Jessell, Columbia University); mouse anti-HOMEOBOX PROTEIN HB9 (HB9) (1/30; DSHB; Cat. No. 81.5C10-c); mouse anti-ISLET1 (ISL1) (1/30; DSHB; Cat. No. 39.4D5-c); rabbit anti-LIMB HOMEOBOX CONTAINING 3 (LHX3) (1/100; Abcam; Toronto, ON, Canada; Cat. No. ab14555), goat anti-FORKHEAD BOX PROTEIN 1 (FOXP1) (1/100; R&D Systems; Cat. No. AF4534), and guinea pig anti-SCIP (1/16,000; kindly provided by Dr. Jeremy Dasen).

Techniques: Derivative Assay, Expressing, Gene Expression

Journal: Biology Open

Article Title: The role of integrin β1 in the heterogeneity of human embryonic stem cells culture

doi: 10.1242/bio.034355

Figure Lengend Snippet: Immunohistochemical analysis of EBs formed from the colonies of hES cells. Six-day-old EBs were fixed with 4% PFA and embedded in 3% agarose for further embedding in paraffin. The cross-sections of the EBs were analysed for the expression (brown colour) of integrin α6 (A), integrin β1 (antibody P5D2, E), the ectodermal marker nestin (B) and the endodermal markers SOX17 (D) and CD184 (F). The nuclei were visualised with Haematoxylin and Eosin staining (blue colour). Haematoxylin and Eosin staining shows the morphology of the EBs (C). The localisation of E-cadherin in a small EB (G), in a more differentiated small EB (H), and in a large EB (I,K). EB with various size visualised by light microscope (J). Immunofluorescence analysis of the cross-sections of the EBs for the ectodermal marker SOX1 (L) and co-staining with SOX1 and brachyury (M). The nuclei were visualised with DAPI staining (L,M). Scale bars: A-I,K, 0.08 mm; J, 0.02 mm; L,M, 0.05 mm.

Article Snippet: Anti-brachyury and anti-SOX1 antibodies were purchased from R&D Systems (Abingdon, UK).

Techniques: Immunohistochemical staining, Expressing, Marker, Staining, Light Microscopy, Immunofluorescence

Journal: PLoS Genetics

Article Title: The RNA helicase DDX6 controls early mouse embryogenesis by repressing aberrant inhibition of BMP signaling through miRNA-mediated gene silencing

doi: 10.1371/journal.pgen.1009967

Figure Lengend Snippet: (A) Whole-mount ISH of E7.5 & E8.5 embryos with a Brachyury probe (Scale: 100 μm, n = 5 for E7.5; 200 μm, n = 16 for E8.5). (B) E6.5 & E7.5 embryo frozen section IHC for BRACHYURY (Scale: 50 μm for E6.5, n = 2; 100 μm for E7.5, n = 3). Embryo parts are indicated by dotted lines. (C) Whole-mount ISH of E8.5 embryos with an Otx2 probe (Scale: 100 μm, n = 3). (D) E6.5 embryo frozen section IHC for SOX1 (Scale: 50 μm for lower magnification, 30 μm for higher magnification, n = 2). Square parts are enlarged in the right panels. Shown with DAPI staining. (E) E8.5 embryo frozen section IHC for SOX1 & SOX2 (Scale: 100 μm, n = 3).

Article Snippet: SOX1 , IHC , 1:100 , NOVUS BIOLOGICALS , AF3369.

Techniques: Staining

Journal: PLoS Genetics

Article Title: The RNA helicase DDX6 controls early mouse embryogenesis by repressing aberrant inhibition of BMP signaling through miRNA-mediated gene silencing

doi: 10.1371/journal.pgen.1009967

Figure Lengend Snippet: Antibodies.

Article Snippet: SOX1 , IHC , 1:100 , NOVUS BIOLOGICALS , AF3369.

Techniques: Concentration Assay, Western Blot

Journal: PLoS Genetics

Article Title: The RNA helicase DDX6 controls early mouse embryogenesis by repressing aberrant inhibition of BMP signaling through miRNA-mediated gene silencing

doi: 10.1371/journal.pgen.1009967

Figure Lengend Snippet: qPCR primer list.

Article Snippet: SOX1 , IHC , 1:100 , NOVUS BIOLOGICALS , AF3369.

Techniques: