DEPDC1 Human Pre-designed siRNA Set A

Cat. No.: D1479747

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Panoramica

DEPDC1 Human Pre-designed siRNA Set A contains three designed siRNAs for DEPDC1 gene (Human), as well as a negative control, a positive control, and a FAM-labeled negative control. Components DEPDC1 siRNA-1: 5 nmol (HPLC) DEPDC1 siRNA-2: 5 nmol (HPLC) DEPDC1 siRNA-3: 5 nmol (HPLC) siRNA Negative Control: 5 nmol (HPLC) FAM-labeled siRNA Negative Control: 5 nmol (HPLC) GAPDH siRNA Positive Control:5 nmol (HPLC)

Specifications

Condizioni di conservazione di stoccaggio

Store at -20°C

Spedito in

Ice chest + Ice pads

Questo prodotto richiede spedizione a catena fredda. I servizi di terra e altri servizi economici non sono disponibili.

Product Line

Prodotti biologici

Application Protocols

No manufacturer‑validated application protocols are provided for this SKU. The following is a generalized workflow for transfecting siRNA into adherent human cells (literature/best practice; adjust per cell line and transfection reagent):

• Reconstitution and aliquoting:
  • Add RNase‑free water or 1× TE to achieve 10–20 µM. Mix gently until fully dissolved. Prepare single‑use aliquots and store at −20 °C.
• Forward transfection (96‑well example):
  1. Seed cells 18–24 h prior to transfection to reach ~40–60% confluence.
  2. Dilute siRNA in 25 µL serum‑free medium per well to reach 2× desired final concentration (e.g., 20–100 nM).
  3. In a separate tube, dilute transfection reagent as recommended (e.g., 0.05–0.2 µL per well) in 25 µL serum‑free medium.
  4. Combine diluted siRNA and reagent; incubate 10–20 min at RT.
  5. Add the 50 µL complex to 50 µL cell medium in each well (final 100 µL).
  6. Incubate 4–6 h (or per reagent IFU), then top up/replace with complete medium if needed.
• Post‑transfection:
  • Assess DEPDC1 mRNA at 24–48 h and protein at 48–96 h.
  • Monitor cell morphology/viability to adjust dose.
• Controls:
  • Include non‑targeting siRNA, positive knockdown control, and mock.

Note: Volumes and reagent amounts vary by platform. Always follow your transfection reagent’s instructions. For any item‑specific directions, refer to the CoA/Spec Sheet.

Biological Roles

This siRNA set targets human DEPDC1 (DEP domain containing 1), enabling functional interrogation of its roles in cellular biology. The following summarizes DEPDC1 biology from the literature (context only; not product performance claims):

• Gene/protein overview (literature):
  • DEPDC1 encodes a cytoplasmic/nuclear protein with a DEP domain implicated in membrane‑proximal signaling and cell cycle regulation.
  • Expression is cell‑cycle regulated, with enrichment during G2/M in several cell types.
• Cellular functions (literature):
  • Reported involvement in mitotic progression, potentially through interactions that influence spindle assembly checkpoint components and transcriptional programs.
  • May participate in NF‑κB–related signaling axes and chromatin‑associated processes in certain contexts.
• Experimental readouts for knockdown (literature/general):
  • mRNA: RT‑qPCR primers spanning exon–exon junctions to quantify DEPDC1 transcript reduction.
  • Protein: antibody‑based detection (WB/IF) if validated antibodies are available; anticipate cell line‑dependent expression levels.
  • Phenotypes: altered cell cycle distribution (e.g., G2/M accumulation), mitotic defects, or proliferation changes depending on model system and perturbation extent.
• Genetic information (literature):
  • Organism: Homo sapiens; gene symbol DEPDC1; alternate names have been reported in databases.

Use this product to transiently reduce DEPDC1 expression for mechanistic studies in vitro. Ensure appropriate controls and orthogonal validation (e.g., independent siRNA sequences or CRISPR) to confirm on‑target effects.

Buffer Applications

While not a buffer component itself, siRNA performance strongly depends on appropriate buffer systems for reconstitution, storage, and transfection complex formation.

• Reconstitution/storage buffers (literature/general):
  • RNase‑free water: convenient for short‑term storage and immediate use.
  • 1× TE (10 mM Tris‑HCl, 0.1–1.0 mM EDTA, pH 7.5–8.0): enhances stability during long‑term frozen storage by chelating divalent cations.
• Transfection complex buffers:
  • Most lipid‑based reagents recommend serum‑free, low‑salt media (e.g., Opti‑MEM) for complex formation, followed by addition to cells in complete medium after 10–30 min incubation (consult your transfection reagent’s IFU).
• Practical recipes (literature):
  • TE buffer: 10 mM Tris‑HCl pH 7.5–8.0, 0.1 mM EDTA in RNase‑free water; filter sterilize (0.22 µm) and store at 4 °C.
• pH/ionic strength considerations:
  • Avoid high salt or divalent cations in stock solutions; they can influence nanoparticle formation with cationic lipids/polymers.
• Electrophoresis/QA:
  • Native PAGE or agarose with appropriate buffers (e.g., TBE) can assess duplex integrity. Handle with RNase‑free reagents throughout.

Item-specific: No buffer formulation information is provided for this SKU; refer to CoA/Spec Sheet for any supplied buffer or recommended reconstitution volumes.

Green Alternatives

Green chemistry considerations are limited for aqueous siRNA workflows but several sustainability practices can reduce environmental impact (general guidance):

• Minimize plastic waste: consolidate plate formats where possible, use reusable cold blocks instead of single‑use ice where permitted, and select low‑plastic transfection setups.
• Choose transfection reagents with documented low cytotoxicity and biodegradability profiles when available; avoid solvent‑intensive formulations.
• Buffer selection: use RNase‑free water or TE prepared in‑house to reduce shipping weight/packaging of premade solutions; prepare only what is needed to limit waste.
• Energy use: store at −20 °C (as required by this item) rather than −80 °C unless specified otherwise; employ frost‑free maintenance and inventory control to reduce door‑open time.
• Waste management: segregate aqueous, nonhazardous oligonucleotide waste from solvent waste; neutralize/denature nucleic acids before disposal if required by local biosafety rules.

Tradeoffs:

• Single‑use RNase‑free plastics are often necessary to avoid contamination; balance waste reduction with data quality and biosafety.
• Shipping on ice packs is needed to maintain integrity; consider consolidated orders and coordinated deliveries to reduce logistics footprint.

Pharmaceutical Uses

This product is for research use only and is not intended for human or veterinary use, diagnostic procedures, or as an active pharmaceutical ingredient.

• Excipient/formulation status: Not applicable; this is a research‑grade siRNA reagent.
• Pharmacopoeia/compendial status: Not specified for this item; refer to CoA/Spec Sheet.
• Manufacturing context (general):
  • In pharmaceutical R&D labs, research‑grade siRNAs are used for target validation, mechanism studies, and assay development in nonclinical systems.
  • Any transition to clinical development would require GMP synthesis, comprehensive impurity profiling, endotoxin/bioburden controls, sterile processing, and regulatory documentation—none of which are claimed for this SKU.

No clinical or therapeutic claims are made for this product.

Physical Properties

• Item-specific facts:
  • Physical state/appearance: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
• General/literature properties for siRNA oligonucleotides (for context only; not product specifications):
  • Form supplied: commonly lyophilized powder or aqueous solution in RNase‑free buffer (literature)
  • Solubility: readily soluble in nuclease‑free water or 1× TE to typical stock concentrations of 10–100 µM (literature)
  • UV absorbance: strong at ~260 nm; A260 used to estimate concentration via sequence‑specific extinction coefficient (literature)
  • pKa/logP: not typically defined for polyanionic polymers like RNA under aqueous conditions (literature)
  • Thermal stability (Tm): duplex Tm depends on length, GC content, and modifications; usually 50–80 °C for ~21‑mer RNA duplexes in physiological salt (literature)
• Practical notes:
  • Reconstitution is best performed with RNase‑free water or 1× TE (0.1–1.0 mM EDTA) to protect from metal‑catalyzed degradation (literature).
  • Avoid repeated freeze–thaw cycles to maintain duplex integrity (literature).

Quality and Grades

• Item-specific details:
  • Grade/purity: Not specified for this item; refer to CoA/Spec Sheet.
  • Appearance and concentration on delivery: Not specified for this item; refer to CoA/Spec Sheet.
• Context for siRNA quality (literature/general; not item specifications):
  • Purification levels commonly used for siRNA include:
    • Desalted: suitable for some screening uses, may contain truncated species.
    • Cartridge/C18 purified: reduced shortmers.
    • HPLC‑purified: high purity, preferred for reproducible knockdown and sensitive assays.
    • PAGE‑purified: highest stringency for demanding applications.
  • Identity/quality control typically includes mass confirmation (MALDI‑TOF/ESI‑MS), OD260 quantitation, and, where applicable, endotoxin bioburden testing for cell‑based assays.
  • Duplex annealing QC: strand stoichiometry and residual single‑stranded content can influence performance.
• Stabilizers/modifications:
  • Common chemical stabilizations (e.g., 2′‑OMe, 2′‑F, phosphorothioates) improve nuclease resistance and reduce innate immune sensing; presence/extent for this item: Not specified for this item; refer to CoA/Spec Sheet.
• Practical guidance:
  • For quantitative phenotyping or low‑abundance targets, select high‑purity, endotoxin‑controlled material.
  • Request/consult the CoA for sequence, purity method, OD, and recommended reconstitution volume specific to this SKU.

Reaction and Applications

Classical organic reaction content is not applicable. As an siRNA pool, the relevant application domain is RNA interference (RNAi) in cell and molecular biology.

• Intended application (item category): pre‑designed siRNAs targeting human DEPDC1 for transient gene knockdown in cultured cells (research use only).
• Typical experimental uses (literature/general):
  • Target validation: assess phenotypic consequences of DEPDC1 reduction in cell models.
  • Pathway analysis: elucidate effects of DEPDC1 on mitotic control, cell cycle progression, and signaling modules.
  • Synthetic lethality and genetic interaction mapping by combining DEPDC1 knockdown with drugs or CRISPR perturbations (screening context).
  • qPCR/RT‑qPCR and Western blot to confirm mRNA and protein reduction; RNA‑seq/proteomics for global impact.
• Practical tips (literature):
  • Use a pool of 3–4 non‑overlapping siRNAs to improve on‑target silencing and reduce off‑target effects.
  • Titrate siRNA (e.g., 5–50 nM final) and optimize cell density, transfection reagent ratio, and exposure time.
  • Include appropriate controls: non‑targeting siRNA, positive knockdown control, and mock transfection.
  • Verify knockdown kinetics: mRNA decline often evident by 24–48 h; protein turnover may require 48–96 h depending on half‑life.
  • Minimize innate immune activation by avoiding high doses and, where applicable, using modified siRNAs.
• Data quality:
  • Replicate at biological and technical levels. Report guide sequences and reagent lots in publications (for this SKU: refer to CoA/Spec Sheet).

Reaction Conditions

In place of chemical reaction conditions, the pertinent parameters are transfection and knockdown conditions (literature/general guidance; optimize per cell line and transfection reagent):

• Stock preparation:
  • Reconstitute to 10–20 µM in RNase‑free water or 1× TE. Vortex gently and briefly spin down. Allow 10 min to fully dissolve.
• Working concentration (final in well):
  • Typical range 5–50 nM; start with 10–25 nM and titrate based on knockdown and cytotoxicity.
• Cell density:
  • Adherent cells at 30–60% confluence for forward transfection; for reverse transfection, seed cells directly onto siRNA–reagent complexes at vendor‑recommended densities.
• Complex formation:
  • Mix siRNA diluted in serum‑free medium (e.g., Opti‑MEM) with diluted transfection reagent; incubate 10–20 min at RT to form complexes.
• Incubation and media changes:
  • Add complexes to cells; after 4–24 h, replace with complete growth medium if required by the reagent.
• Assay timing:
  • mRNA knockdown assessment at 24–48 h by RT‑qPCR; protein reduction often at 48–96 h depending on protein half‑life.
• Controls:
  • Non‑targeting siRNA, positive knockdown control, and transfection‑only control.
• Replicates and statistics:
  • Perform ≥3 biological replicates; analyze with appropriate statistical tests.

Item-specific conditions (e.g., exact sequences, recommended dose): Not specified for this item; refer to CoA/Spec Sheet.

Safety and Handling

• Item-specific safety data:
  • GHS classification, signal word, H‑statements, pictograms: Not specified for this item; refer to SDS.
• General guidance for siRNA/oligonucleotides (literature/best practice; defer to SDS):
  • Expected hazards: siRNAs are non-volatile, non-flammable biopolymers with low acute toxicity; treat as laboratory chemical/biological material.
  • PPE: lab coat, safety glasses, and disposable nitrile gloves. Change gloves frequently to prevent RNase contamination.
  • Handling: work in a clean area dedicated to RNA work. Use RNase‑free consumables and solutions. Wipe surfaces/equipment with RNase decontamination agents.
  • Incompatibilities: avoid RNases (ubiquitous), strong acids/bases, and nucleases; avoid prolonged exposure to high temperatures.
  • First aid (general):
    • Skin/eyes: rinse with water if contacted. Remove contaminated clothing. Seek medical attention if irritation persists.
    • Ingestion/inhalation: unlikely exposure routes; seek medical advice if symptoms occur.
  • Spill/cleanup: absorb aqueous solutions with disposable towels, dispose according to institutional guidelines for nonhazardous laboratory waste. Decontaminate surfaces for RNase.
  • Waste: follow local regulations. Small quantities can generally be disposed as nonhazardous aqueous organic waste; verify with EHS.
• Transport/storage risks:
  • Maintain cold chain per item data (ice packs during shipment; store at −20 °C). Protect from repeated freeze–thaw.
• Always consult the SDS for authoritative safety information.

Solvent Selection

Because this product is an siRNA reagent, organic solvent selection is not typically applicable. Instead, focus on nuclease‑free aqueous buffers for reconstitution and use.

• Item-specific note: No formulation details provided. Refer to CoA/Spec Sheet for any supplied buffer information.
• Recommended reconstitution media (literature/general):
  • RNase‑free water: suitable for most transfections; prepare fresh or use certified RNase‑free.
  • 1× TE (10 mM Tris‑HCl, 0.1–1.0 mM EDTA, pH 7.5–8.0): EDTA chelates divalent cations, enhancing stability during storage.
  • PBS is generally avoided for stock solutions due to divalent cations and salts that may affect complexation with some transfection reagents.
• Working solutions:
  • Prepare working dilutions (e.g., 5–50 nM final in wells; literature) in serum‑free transfection medium immediately before use.
• Compatibility with transfection reagents:
  • Most lipid/polymer transfection reagents require serum‑free conditions during complex formation; check the reagent manufacturer’s instructions.

Small comparison (literature):

• RNase‑free water: maximum versatility; lowest ionic strength; ideal for stock preparation.
• 1× TE: improves long‑term stability at −20 °C; EDTA may interfere with cationic delivery agents if not sufficiently diluted in the final mix.

Storage and Reconstitution

• Item-specific storage/shipping (from Product Data):
  • Storage conditions: Store at −20 °C.
  • Shipped in: Ice chest + ice pads.
• Reconstitution (general guidance; not item specifications):
  • Use RNase‑free water or 1× TE to prepare 10–20 µM stock solutions. Gently flick/vortex briefly and spin down; allow to sit on ice for 5–10 min to ensure complete dissolution.
  • If provided lyophilized, determine volume from the OD260/µmol data on the CoA (Not specified for this item; refer to CoA/Spec Sheet).
• Aliquoting and storage:
  • Prepare single‑use aliquots to avoid freeze–thaw cycles. Store aliquots at −20 °C (short–medium term). For extended storage, some labs keep at −80 °C (literature); follow internal practices.
  • Protect from RNases: use certified RNase‑free tubes and barrier tips; clean work area with RNase decontamination solution.
  • Avoid repeated freeze–thaw to prevent strand degradation and loss of activity.
• Working solutions:
  • Prepare immediately before use in serum‑free medium for complex formation. Discard any unused working solution; do not refreeze diluted siRNA.
• Stability (general):
  • siRNA duplexes are stable for months at −20 °C when properly aliquoted and stored desiccated or in TE (literature). Exact shelf life for this SKU: Not specified for this item; refer to CoA/Spec Sheet.

Always consult the CoA/SDS accompanying SKU D1479747 for definitive, item‑specific instructions.

Structure and Identity

Short description: DEPDC1 Human Pre-designed siRNA Set A is a research-grade pool of double‑stranded small interfering RNAs (siRNAs) designed to transiently silence human DEPDC1 mRNA via the RNA interference pathway.

• Item-specific facts (from Product Data):
  • Product name: DEPDC1 Human Pre-designed siRNA Set A (SKU: D1479747)
  • Intended target: human DEPDC1 (DEP domain containing 1) mRNA
  • Storage: −20 °C
  • Shipped: Ice chest + ice pads
  • Research use only
• Not specified for this item; refer to CoA/Spec Sheet:
  • Exact siRNA sequences, sense/antisense strand lengths and modifications
  • Molecular formula, molecular weight, and any stabilizers
  • CAS, CID, SMILES, InChIKey
• Structural features (general literature for siRNA):
  • Typical siRNA: ~21–23 nt double-stranded RNA duplex with 2‑nt 3′ overhangs (e.g., UU) and 5′-phosphate groups (literature)
  • Sense and antisense strands are complementary; antisense strand guides RISC to target mRNA (literature)
  • May include backbone or sugar/base modifications to enhance stability and reduce off‑targeting; specific modifications for this item: Not specified for this item; refer to CoA/Spec Sheet.
• 2D description (general): two antiparallel RNA strands forming a short A‑form duplex; no classical small‑molecule line notation (SMILES/InChI) applies (literature).

Synthetic Utility

Classical organic/organometallic synthetic utility does not apply to this product. As a biological oligonucleotide reagent, it serves as a functional tool for gene expression knockdown rather than a building block in chemical synthesis.

• Relevant laboratory use (general):
  • Tool compound for perturbing DEPDC1 levels in cell culture to study pathways, validate targets, or benchmark assay responsiveness.
  • Can be combined with small‑molecule inhibitors or genetic tools to map pathway dependencies (systems biology context).

For chemical synthesis applications (e.g., coupling, catalysis, polymerization), please refer to other categories in the catalog better suited to those workflows.

Target Specificity

• Item-specific details:
  • Intended gene target: human DEPDC1 (DEP domain containing 1).
  • Species reactivity: Homo sapiens (by design context). Specific target regions/sequences: Not specified for this item; refer to CoA/Spec Sheet.
• General considerations for siRNA specificity (literature):
  • Use pools of non‑overlapping siRNAs to enhance on‑target suppression and dilute off‑target seed effects.
  • BLAST alignment of guide strands against the human transcriptome is recommended to screen for potential off‑target complementarity.
  • Seed‑region (positions 2–8) complementarity drives many off‑target events; chemical modifications (e.g., 2′‑OMe in seed) can mitigate these.
  • SNPs and splice variants may affect knockdown efficiency; confirm the expressed isoforms in your cell model.
• Validation workflow:
  • Confirm mRNA depletion by RT‑qPCR with multiple primer sets.
  • Rescue experiments with siRNA‑resistant DEPDC1 cDNA add confidence to target specificity.

For definitive item‑level targeting information (guide sequences, target exons, modification patterns), consult the CoA/Spec Sheet for SKU D1479747.

Domande frequenti

How should this product be stored?

Store at ?20 °C. Freezer storage is required to maintain the specified shelf life.

How is this product shipped?

This product ships in an insulated container with ice pads. Unpack on arrival and transfer it to the storage condition stated above.

What documentation is provided?

Available product documentation, including Certificates of Analysis (COA), Safety Data Sheets (SDS), and specification sheets, is shown in the product document area. Document availability and access follow the current site policy.