The largest database of trusted experimental protocols

35 protocols using xylol

1

Paraffin Embedding of in situ Hybridized Embryos

Check if the same lab product or an alternative is used in the 5 most similar protocols
On completion of in situ hybridization staining, embryos were fixed overnight in 4% PFA at 4 °C. Embryos were washed two times in PBST, then placed in plastic cryomoulds. PBST was removed and molten 1% agarose/PBS was added. Embryos were correctly orientated and left for 1 h to allow the agarose to set. The agarose block was removed from the mould and dehydrated serially in 70, 90, 95, 100% ethanol (Sigma-Aldrich) for 1 h each. The block was cleared in 50:50 ethanol:xylol (Sigma-Aldrich) then 100% xylol for 1 h each. To begin paraffin infiltration, the block was left in 50:50 xylol:HistosecParaffin (MerckMillipore) overnight at 60 °C. Hundred per cent paraffin was added and changed twice daily for 3 days. The block was then mounted on a holder and left at room temperature overnight before 6-μm sections were cut on a microtome. Sections were placed on a slide and mounted under a coverslip with Entellan (ThermoFisher).
+ Open protocol
+ Expand
2

TUNEL Assay for Apoptosis Detection

Check if the same lab product or an alternative is used in the 5 most similar protocols
Apoptosis was determined by terminal deoxynucleotidyl transferase-mediated dUTP end labeling (TUNEL) which detects the DNA fragments of apoptotic cells. TUNEL staining was performed with the In Situ Cell Death Detection Kit (Roche Molecular Chemical, cat. number 11684817910). Briefly, the sections were dewaxed and rehydrated in xylol (Sigma, Germany) and a graded series of 100%, 90%, 80%, and 70% ethanol. Endogenous peroxidase activity was blocked by incubating with 0.3% H2O2 in methanol for 30 min. For permeabilization of tissue, the sections were incubated with 20 μg/mL proteinase K (Roche, Germany) in 10 mM Tris HCl (pH 7.5) for 10 min at room temperature. Then, the sections were incubated in 50 μL of TUNEL solution (In Situ Cell Death Detection Kit, Roche, Germany) for 1 h at 37°C. After incubation with converter POD, HRP for 1 h at 37°C, the sections were incubated with DAB (Sigma, Germany) chromogen at 37°C. Cells were counterstained with hematoxylin (Sigma, Germany) for 20 s. Sections were dehydrated in a graded series of 70%, 80%, 90%, and 100% ethanol and cleared in xylol for 15 min. After mounting the sections were examined by a light microscope.
+ Open protocol
+ Expand
3

DNA Extraction from FFPE Tissue

Check if the same lab product or an alternative is used in the 5 most similar protocols
Commercially available QIAamp DNA FFPE Tissue Kit (Qiagen) was used. The steps of the experiment were done according to the product insert provided by the manufacturer. Xylol (Sigma-Aldrich, Germany) was used to dissolve the paraffin and 98–100% ethanol (Sigma-Aldrich, Germany) was used to remove the Xylol and to reconstitute the buffers. The concentration of the extracted pure DNA was measured spectrophotometrically (Ultraspec® 1000, Amersham Pharmacia Biotech, Cambridge, England) at 260 nm and the DNA samples were stored at − 80 °C until the time of DNA sodium bisulfite treatment.
+ Open protocol
+ Expand
4

Histological Analysis of Corneal Tissues

Check if the same lab product or an alternative is used in the 5 most similar protocols
The corneas were fixed in 4% paraformaldehyde (PFA; Santa Cruz, DBA, Italy) overnight and washed in 7.5, 15 then 30% sucrose solution sequentially for 30 min each. The corneas were then incorporated in optimal cutting temperature compound, flash frozen and stored at −80°C. Sections (10 μm) were obtained for histological and immunofluorescence. Haematoxylin and eosin staining was performed for standard histology. Fixed samples (4% PFA) were rehydrated in distilled water, exposed to Harris haematoxylin (Sigma Aldrich, Milan, Italy) for 8 min and then washed three times with tap water for 5 min each. Differentiation solution (Sigma‐Aldrich, Italy) was added then the samples were briefly washed with tap water. Samples were further exposed to Eosin (Sigma‐Aldrich, Italy) for 2 min then washed with tap water as before. Sections were washed in an increasing concentration of alcohol (70, 90 and 100%) followed by xylol (Sigma‐Aldrich, Italy) treatment for 3 min each. Xylene‐based mounting medium (Sigma‐Aldrich, Italy) was used to mount and preserve the samples, which were examined using light microscopy. ZEN software was used to capture the images.
+ Open protocol
+ Expand
5

EAE Induction and In Vitro Assays

Check if the same lab product or an alternative is used in the 5 most similar protocols
RPMI-1640 medium, penicillin/streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Invitrogen, Germany). Hooke kit for EAE induction (myelin oligodendrocyte glycoprotein35-55 (MOG35-55) (20 (link)) combined with complete Freund’s adjuvant (CFA) emulsion (21 (link)) and pertussis toxin (PTX):5X) and MOG35-55 for in vitro stimulation of cells were purchased from Hooke laboratories (EK-0115, Lawrence, MA, USA). Reagents required for histopathological analyses including paraffin, xylol, alcohol, phosphate buffer saline (PBS) and Luxol fast blue were obtained from Sigma (Sigma-Aldrich, Germany). IL-6 ELISA kit and cell proliferation ELISA BrdU kit were obtained from e-Bioscience and Roche, respectively. MS14, an Iranian herbal-marine compound classified as equivalent to food with no observable adverse effect level (NOAEL), was donated by deceased Dr. Ahmadi.
+ Open protocol
+ Expand
6

Paraffin-Embedded Tissue Histology Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
Formalin-fixed tissue specimens were embedded in paraffin. Tissue sections (5-μm thick) were deparaffinized in xylol (534056; Sigma-Aldrich) and rehydrated in serial alcohols and were later used for hematoxylin-eosin (HE) (hematoxylin, 104302; eosin, 115935; Merck KGaA, Darmstadt, Germany) staining and double immunostaining (DakoCytomation EnVision®, Doublestain System [HRP-AP], Dako Inc., Carpinteria, CA, USA). Digital images of HE and immunostained sections were made on a Photomicroscope Olympus (Olympus BX41TF; Olympus, Tokyo, Japan) with a digital camera (Olympus C5060; Olympus) for the acquisition and analysis of the images.
+ Open protocol
+ Expand
7

Hematoxylin and Eosin Staining of Cell Sheets

Check if the same lab product or an alternative is used in the 5 most similar protocols
Hematoxylin and eosin (Sigma-Aldrich, St Louis, USA) staining of cell sheets was also performed. Briefly, after detachment and fixation in 4% paraformaldehyde (Sigma-Aldrich, St Louis, USA) for 24 h, samples were paraffin embedded and sectioned in 4 µm thickness. After the sectioning process, the histological samples were placed in a water bath at 50 °C and captured to a histological slide and stored in an oven at 65 °C for 12 h to allow the paraffin remnants to be removed. Sequentially, paraffin removal dehydration protocol was completed using a sequence of xylol (Sigma-Aldrich, St Louis, USA) and alcohol (Sigma-Aldrich, St Louis, USA) solutions and the specimens proceeded a routine H&E staining following the manufacturer's guidelines.
+ Open protocol
+ Expand
8

FFPE DNA Extraction and QC

Check if the same lab product or an alternative is used in the 5 most similar protocols
Before DNA extraction, 10 µm thin FFPE slices were deparaffinized using xylol (Sigma-Aldrich) and then washed with ethanol 99-100% (Sigma-Aldrich). DNA extraction was performed using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer's protocol. The quality and concentration of all DNA samples were assessed using NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Inc.).
+ Open protocol
+ Expand
9

Histological Analysis of Blastocyst Development

Check if the same lab product or an alternative is used in the 5 most similar protocols
Conceptus samples were fixed in 4% paraformaldehyde (Sigma-Aldrich, St. Louis, MO, USA) for 24 h, dehydrated in dilutions (70%-100%) of ethanol (Sigma-Aldrich), and embedded in paraffin (Tolosa et al., 2003 ). Sections of 5 μm were cut and mounted. Sections were stained using hematoxylin and eosin (Sigma-Aldrich) to investigate blastocyst, surrounding endometrium and embryonic layers formation morphology. Following deparaffinization in xylol (Sigma-Aldrich, Wicklow, Ireland) at room temperature (RT) using two solutions for 10 min each, rehydration in a descending series of etanol concentrations was performed (100%, 2 × 5 min; 5 min each for 90%, 80%, and 70%), followed by distilled water (RT, 5 min). The sections were then stained with hematoxylin for 30 s at RT, washed in running water for 10 min, stained with eosin at RT for 15 s, and washed in running water for 10 min. The slides were then dehydrated in increasing dilutions of ethanol (RT, 5 min 70%, 5 min 80%, 5 min 90%, 2 × 5 min 100%), cleaned in xylene (Sigma-Aldrich) at RT, 2 × 10 min, and mounted on Permount® (SP15-500; Thermo Fisher Scientific, Waltham, MA, USA). The analyses were performed by light microscopy (Nikon Eclipse 80i, Tóquio, Japão).
+ Open protocol
+ Expand
10

Toluidine Blue Staining of Cultured Slices

Check if the same lab product or an alternative is used in the 5 most similar protocols
Slice cultures were fixed in paraformaldehyde (4%, 0.1 M phosphate buffer; Applichem, Darmstadt, Germany) and rinsed in 0.1 M phosphate-buffered salt solution (PBS). Thereafter, slice cultures were exposed for 20 min to toluidine-blue working solution, which was a mixture of 5 ml stock solution (1 g of Toluidine Blue O in 100 ml of 70% ethanol; Sigma-Aldrich) and 45 ml of 1% NaCl solution (pH 2.0–2.5). Thereafter, 96% ethanol (100 ml of 96% ethanol and 4 drops of acetic acid) was used for color-differentiation of the staining. The differentiation step with strong acid removes unspecific staining of weak acidic structures and, thus, increases the contrast between background and stained cells. The process was stopped using 0.1 M PBS, once the differentiation was clearly visible. After brief rinsing with double distilled water, slice cultures were placed on object plates and dried overnight. The slices were then exposed to xylol (Sigma-Aldrich) for 10 min and embedded with Entellan Neu (Merck Millipore, Schwalbach, Germany).
+ Open protocol
+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!