A milestone in virtual cell modeling: Recently, Leman Bio will officially launch the “ELEM‑1200RS,” a large-scale bulk perturbation transcriptomic atlas designed for the Virtual Cell Challenge, marking a major breakthrough in gene perturbation modeling, virtual cell research, and drug target discovery.

 

A milestone for virtual‑cell builders: We have released ELEM‑1200RS, a large‑scale bulk RNA-seq perturbation atlas built for the Virtual Cell Challenge. This is a major leap forward for genetic‑perturbation modelling, virtual cell research, and therapeutic target discovery.

 

Background material: AIVC Special Feature | AIVC Enters the Data Competition: Who Can Provide Verifiable Cell Perturbation Data?

 

Instructions for Downloading the ELEM-1200RS Dataset

I. Dataset Overview

The ELEM Biotech (Liman Bio) virtual cell perturbation transcriptomics dataset, “ELEM-1200RS,” comprises approximately 1,200 bulk RNA‑seq samples derived from 63 wild-type cell line backgrounds, with knockdown experiments targeting a total of 914 unique genes. Gene expression data are provided as TPM‑normalized expression matrices in .h5ad format, consistent with the data structure used in the Virtual Cell Challenge.

 

The dataset is published on the Hugging Face platform and is available during the priority access period. “Access Control Mode” Manage download permissions.

Dataset access URL: https://huggingface.co/datasets/ELEM-Bio/ELEM-1200RS

Note: The publicly released datasets do not include mappings between sample IDs and the target genes or cell line names affected by perturbations. To obtain the complete annotated metadata, please submit a request to ELEM at sales@elem-bio.com; upon verification, we will provide the corresponding annotation information.

Figure 1. Differences between the Arrayed Library gene perturbation dataset and the Pooled Library gene perturbation dataset.

 

II. Download Procedure During the Priority Access Period

(September 30, 2026 to October 12, 2026, Beijing Time, UTC+8)

During the priority access period, the dataset is made available to designated partner teams that have signed the “AIVC Data Priority Access and Use Agreement.” Free Priority access and usage rights are provided; the download procedure is as follows:

1. Log in to the Hugging Face platform, visit the link above, or search for the dataset name “ELEM-1200RS” to access the dataset’s homepage.

2. On the dataset’s “Dataset card” page, please click “Agree and send request to access repo” to submit your data access request.

3. Please send your Hugging Face username, registered email address, and other relevant information to our email address sales@elem-bio.com. Refer to the email template in Section 4, “Application Email Template (1. Priority Access Period).”

4. Upon receiving your email, ELEM will grant you access to the data and provide the complete annotated metadata accompanying the expression matrix. You will receive a notification email from the Hugging Face system, after which you can log in to the platform to download the dataset.

Note: Teams applying for priority access to the data should send an email to yongbo_cheng@elem-bio.cn to obtain the “AIVC Data Priority Access and Use Agreement” and complete the signing of the agreement between September 24, 2026, and September 30, 2026.

 

III. Fully Publicly Released Download Procedure

(Effective October 13, 2026, Beijing Time, UTC+8)

Effective October 13, 2026, ELEM will make this dataset publicly available worldwide, and users will no longer need to request access. The download procedure is as follows:

1. Log in to the Hugging Face platform, visit the link above, or search for the dataset named “ELEM-1200RS” to access the dataset’s homepage.

2. On the “Files and versions” page of the dataset, you can directly download the corresponding dataset.

3. Please send your Hugging Face username, registered email address, and other relevant information to our email address sales@elem-bio.com. Refer to the email template in Section 4, “Application Email Template (2. During Public Release).”

4. Upon receipt of the email, ELEM will provide the complete annotated metadata accompanying the expression matrix.  

 

IV. Application Email Template

1. Priority Access Period

Recipient : sales@elem-bio.com

Email Subject : ELEM-1200RS Annotation Information Request

Email body ：

ELEM Biotech Team,

We have signed the “AIVC Data Priority Access and Use Agreement” and have submitted a download request for the virtual cell perturbation transcriptomics dataset ELEM‑1200RS on the Hugging Face platform. We now request access to the mapping annotations of perturbation target gene names and cell line names, which are intended for use in ( Please briefly state the purpose of your research/use. ).

Applicant’s Name:

Unit/Team:

Hugging Face username:

Contact email:

Contact phone number:

 

2. During the public release period

Recipient : sales@elem-bio.com

Email Subject : ELEM-1200RS Annotation Information Request

Email body ：

ELEM Biotech Team,

We have already downloaded the virtual cell perturbation transcriptomics dataset ELEM‑1200RS from the Hugging Face platform. We now request access to the mapping annotations that associate perturbation target gene names with cell line names, which we intend to use for ( Please briefly state the purpose of your research/use. ).

Applicant’s Name:

Unit/Team:

Hugging Face username:

Contact email:

Contact phone number:

 

 

ELEM-1200RS Dataset Download Instructions

 

1. Dataset Overview

The ELEM Biotech Virtual Cell Perturbation Transcriptomics Dataset ("ELEM-1200RS") comprises approximately 1,200 bulk RNA-seq samples derived from 63 wild-type cell lines, with knockdown experiments targeting 914 unique genes. Gene expression data are provided as TPM-normalized expression matrices in .h5ad format, consistent with the data structure adopted by the Virtual Cell Challenge.

The dataset is released on the Hugging Face platform. During the priority access period, download permissions are administered through gated access.

Dataset URL: https://huggingface.co/datasets/ELEM-Bio/ELEM-1200RS

 

Note: The publicly released dataset does not include the mapping between sample IDs and the corresponding target-gene names or cell line names. To obtain the complete annotation metadata, please submit your request to ELEM via email: sales@elem-bio.com.The corresponding annotation information will be provided upon confirmation.

 

2. Download Procedure During the Priority Window

(September 30, 2026 to October 12, 2026, Beijing Time, UTC+8)

During the priority window, the dataset is made available free of charge for priority access and use to designated collaboratingteams that have executed the Dataset Priority Use Agreement. The download procedure is as follows:

1. Log in to the Hugging Face platform. Navigate to the link provided above, or search for the dataset name 'ELEM‑1200RS' to access the dataset homepage;

2. On the 'Dataset card'page, click 'Agree and send request to access repo'to submit your data access application;

3. Send your Hugging Face username, registered email address, and other relevant information to sales@elem-bio.com. An email template is provided in Section 4.1 (Priority Window);

4. Upon receipt of your email, ELEM will grant you dataset-access permissions and provide the annotation metadata accompanying the expression matrix. Hugging Face will notify you when access is granted, after which you may log in to download the dataset.

Note: Teams wishing to apply for priority data access and usage should email yongbo_cheng@elem-bio.cn to obtain the "AIVC Data Priority Access and Usage Agreement" and complete the signing of the agreement between September 24, 2026, and September 30, 2026.

 

3. Download Procedure Following the Global Public Release

(Effective October 13, 2026, Beijing Time, UTC+8)

Effective October 13, 2026, ELEM will publicly release the dataset worldwide. The download procedure is as follows:

1. Log in to the Hugging Face platform. Navigate to the link provided above, or search for the dataset name 'ELEM‑1200RS' to access the dataset homepage;

2. You may directly download the dataset files from the 'Files and versions'page;

3. Send your Hugging Face username, registered email address, and other relevant information to sales@elem-bio.com. An email template is provided in Section 4.2 (Public Release Period);

4. Upon receipt of your email, ELEM will provide the annotation metadata accompanying the expression matrix.

 

4. Email Templates

 

1. Priority Window

Recipient: sales@elem-bio.com

Subject: Request for ELEM-1200RS metadata

Email Body :

Dear ELEM Biotech Team,

We have executed the AIVC DATA PRIORITY ACCESS AND USE AGREEMENT and have submitted a download request for theVirtual Cell Perturbation Transcriptomics Dataset 'ELEM-1200RS' on the Hugging Face.

We hereby request the corresponding mapping metadata for the perturbed target-gene names and cell line names. This information will be used for the following research purpose: (please briefly state your research/use purpose).

 

Applicant name:

Institution/Team:

Hugging Face username:

Contact email:

telephone:

Best regards

 

2. Public Release Period

Recipient: sales@elem-bio.com

Subject : Request for ELEM-1200RS metadata

Email Body :

Dear ELEM Biotech Team,

We have downloaded the Virtual Cell Perturbation Transcriptomics Dataset 'ELEM-1200RS' from Hugging Face. We hereby request the corresponding mapping metadata for the perturbed target-gene names and cell line names. This information will be used for the following research purpose: (please briefly state your research/use purpose).

 

Applicant name:

Institution/Team:

Hugging Face username:

Contact email:

telephone:

Best regards