Additional file 6: of Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish

Comprises of the details of the predicted novel miRNAs of all the samples including the IDs, miRDeep2 scores, read counts, precursor and mature sequences and precursor coordinates. Sheet1: embryo predicted novel miRNAs, Sheet2: male brain predicted novel miRNAs, Sheet3: female brain predicted novel miRNAs, Sheet4: male gut predicted novel miRNAs, Sheet5: female gut predicted novel miRNAs, Sheet6: male liver predicted novel miRNAs, Sheet7: female liver predicted novel miRNAs, Sheet8: ovary predicted novel miRNAs, Sheet9: testis predicted novel miRNAs, Sheet10: eye predicted novel miRNAs, Sheet11: heart predicted novel miRNAs). (XLSX 159 kb

Additional file 12: of Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish

Comprises of additional details of the methods, including the options and parameters of the tools used for processing of the reads, known miRNA expression profile generation, normalization and clustering and novel miRNA prediction pipeline. (PDF 1468 kb

Additional file 7: of Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish

Figure showing the structure of a predicted novel miRNA from miRdeep2 with its aligned read sequences. MiRdeep2 gives as output the pdfs of the structure of the predicted novel miRNA along with the reads mapping to its mature, star and loop sequences. The top left corner has the score distribution for the predicted novel miRNA, the top right corner has the predicted hairpin structure for the novel pre-miRNA and the major part comprises of the alignment of the reads to the mature (red), loop (yellow) and the star regions (purple) of the precursor miRNA. For each read mapped, its frequency value, the number of mismatches with which it maps, and the sample it belongs to is given at the bottom right. (PDF 221 kb

El Distrito Universitario : Semanario de 1ª Enseñanza: Año XXI Número 1066 - 1923 abril 12

Copia digital. Madrid : Ministerio de Cultura. Subdirección General de Coordinación Bibliotecaria, 200

CD44 Is a Negative Cell Surface Marker for Pluripotent Stem Cell Identification during Human Fibroblast Reprogramming

<div><p>Induced pluripotent stem cells (iPSCs) are promising tools for disease research and cell therapy. One of the critical steps in establishing iPSC lines is the early identification of fully reprogrammed colonies among unreprogrammed fibroblasts and partially reprogrammed intermediates. Currently, colony morphology and pluripotent stem cell surface markers are used to identify iPSC colonies. Through additional clonal characterization, we show that these tools fail to distinguish partially reprogrammed intermediates from fully reprogrammed iPSCs. Thus, they can lead to the selection of suboptimal clones for expansion. A subsequent global transcriptome analysis revealed that the cell adhesion protein CD44 is a marker that differentiates between partially and fully reprogrammed cells. Immunohistochemistry and flow cytometry confirmed that CD44 is highly expressed in the human parental fibroblasts used for the reprogramming experiments. It is gradually lost throughout the reprogramming process and is absent in fully established iPSCs. When used in conjunction with pluripotent cell markers, CD44 staining results in the clear identification of fully reprogrammed cells. This combination of positive and negative surface markers allows for easier and more accurate iPSC detection and selection, thus reducing the effort spent on suboptimal iPSC clones.</p></div

CD44 expression is gradually lost during fibroblast reprogramming.

<p>Flow cytometry dot plots with CD44-Alexa Fluor® 488 signal on the x-axis and SSEA4-Alexa Fluor® 647 signal on the y-axis. Lines demarcate quadrants of negative and positive signals for the two fluorophores, and the numbers at each corner indicate the percentage of cells per quadrant. The data compare (A) parental BJ fibroblasts, (B) H9 ESCs, (C) Day 9 reprogramming samples, and (D) Day 26 reprogramming samples.</p

Additional file 10: of Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish

Figure showing the schematic representation of obtaining specific novel pre-miRNAs for embryo. The coloured circles represent the set of predicted novel pre-miRNAs for each tissue sample. The 78 predicted novel pre-miRNAs of embryo were compared with the set of predicted novel pre-miRNAs of other tissues to find the ones that matched. The total set of matched novel pre-miRNAs were 59. Therefore the unmatched set of 19 was considered as specific novel pre-miRNAs for embryo. This procedure was followed for the other tissue samples to obtain the novel pre-miRNAs specific to them. (PDF 30 kb

Fully reprogrammed and partially reprogrammed clones are distinguished by combining multiple methods of characterization.

<p>(A) iPSC clones generated from BJ fibroblasts and characterized for the presence of pluripotent markers AP, SSEA4 and TRA-1-60. Figure shows phase contrast and fluorescence images merged together (Scale bar: 200 µm). (B) Principal Component Analysis of the global gene expression data from the controls and the iPSCs generated in the study. The three major clusters are demarcated by the red, green, and dark blue boxes. The dark blue and light blue boxes indicate the same clones, but at P5 and P16/17, respectively. (C) Pluripotency scores obtained using PluriTest^TM analysis of the global gene expression data for the cells used in the study. The area marked by red lines depicts the region under which 95% of pluripotent samples are expected to fall, while the region between the blue lines depicts where 95% of non-pluripotent samples fall. The dark blue and light blue boxes again indicate the same clones, but at early and late passages, respectively. (D) Immunostaining of trilineage differentiation markers AFP, βIIITub and SMA (red) in Day 21 differentiated ESCs and iPSCs used in the study (Scale bar: 200 µm).</p

Additional file 3: of Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish

Comprises of the details of the sex associated known miRNAs including the logFC, logCPM, P-value and FDR values. Sheet1: brain, Sheet2: gut, Sheet3: liver, Sheet4: ovary vs. testis. (XLSX 20 kb

Description of parental BJ fibroblasts, control pluripotent H9 ESCs and episomal iPSCs, and iPSC clones used in the study.

<p>ND  =  Not determined.</p