> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009527.md).
# Assessing library QC in Illumina Single Cell 3' RNA Prep
**Library Yield Expectations**
Library yield depends on several factors, including sample type, cell/nuclei input, and PCR cycle number used during the Amplify Library step of the Illumina Single Cell (SC) 3' RNA Prep workflow.
Refer to [Illumina Single Cell 3' RNA Prep library QC best practices](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009526.md) to confirm accurate QC assessment.
Adjust the number of PCR cycles used during the Amplify Library program to optimize for different input quality and concentration. Review the [Illumina Single Cell 3' RNA Preparation library sequencing recommendations](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009449.md) and confirm the minimum yield required for optimal sequencing performance.
For more information on recommended PCR cycling parameters, refer to [Selecting cycle numbers for High and Low RNA sample types with Illumina Single Cell RNA prep kits](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009521.md)
**Final Library QC Expectations and Assessment Best Practices**
The final Illumina SC 3' RNA Prep library is expected to have an **average fragment size ranging between 370**-**550 bp when the region table is set from 200 to 800 bp**.
Library distributions and average fragment size may vary based on sample type and experimental conditions. Refer to [Representative library QC traces for Illumina Single Cell 3' RNA Prep](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009528.md) for additional examples from different sample types.
**Figure 1**. Representative fragment analysis of an Illumina Single Cell 3' RNA Prep T2 library from a 5,000-cell HEK 293T/NIH 3T3 mixture using a HS D1000 ScreenTape.
If there are adapter peaks remaining in the final library, these can significantly reduce sequencing efficiency. If these are present, Illumina recommends performing an additional 0.8X magnetic bead cleanup. This extra size selection is not recommended if the library prep concentrations are low. See [0.8X bead cleanup to remove adapter dimers from Illumina Single Cell 3’ RNA Prep libraries](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009534.md) for more information.
Refer to Section 3.2: *Quality Checks* of the [Illumina Single Cell 3' RNA Prep Training Packet](https://support.illumina.com/content/dam/illumina-support/courses/illumina-single-cell-3-rna-prep-training-packet/illumina-single-cell-3-rna-prep-training-packet-200065159-02.pdf) on the [Illumina Single Cell Prep Support page](https://support.illumina.com/sequencing/sequencing_kits/illumina-single-cell-prep.html) (under the Training heading) for information on final library assessment.
\
\
\
| |
| :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #9527), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009527%20-%20Library%20Preparation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |
---
# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.
## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.
Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:
```
GET https://knowledge.illumina.com/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009527.md?ask=&goal=
```
`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.
Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.