Update README.md

README.md

@@ -14,15 +14,15 @@ configs:
 
 # X-Atlas/Orion 
 
-X-Atlas: Orion edition (X-Atlas/Orion) is a Perturb-seq atlas containing two genome-wide Fix-Cryopreserve-ScRNAseq (FiCS) Perturb-seq screens in HCT116 and HEK293T cells 
-that target all human protein-coding genes (n = 18,903 genes). X-Atlas/Orion is comprised of eight million cells that are deeply sequenced to over 16,000 unique molecular identifiers 
-(UMIs) per cell and contain a median on-target knockdown efficiency of 75.4% and 51.5% in HCT116 and HEK293T, respectively. Through the release of X-Atlas/Orion, we highlight the 
-potential of FiCS Perturb-seq to address current scalability and variability challenges in data generation, advance foundation model development that incorporates gene-dosage effects, 
-and accelerate biological discoveries.
+X-Atlas: Orion edition (X-Atlas/Orion) is a Perturb-seq atlas containing two genome-wide Fix-Cryopreserve-ScRNAseq (FiCS) Perturb-seq screens that target all human 
+protein-coding genes (n = 18,903 genes). The dataset is comprised of eight million HCT116 and HEK293T cells, each deeply sequenced to a median of 16,000 unique molecular 
+identifiers (UMIs) per cell. The median on-target knockdown efficiency is 75.4% in HCT116 cells and 51.5% in HEK293T cells, with a median of at least 140 cells per 
+perturbation. Through the release of X-Atlas/Orion, we highlight the potential of FiCS Perturb-seq to address current scalability and variability challenges in data 
+generation, advance foundation model development that incorporates gene-dosage effects, and accelerate biological discoveries.
 
 **Preprint**: [X-Atlas/Orion: Genome-wide Perturb-seq Datasets via a Scalable Fix-Cryopreserve Platform for Training Dose-Dependent Biological Foundation Models](https://www.biorxiv.org/content/10.1101/2025.06.11.659105v1)
 <br>
-**h5ads**: https://doi.org/10.25452/figshare.plus.29190726
+**Processed h5ads and other metadata**: https://doi.org/10.25452/figshare.plus.29190726
 
 <img src="https://pbs.twimg.com/media/Gt6v0cfXkAAUCkc?format=jpg&name=large" width="1024" height="1024">
 
@@ -44,8 +44,8 @@ The dataset contains the following information:
 
 | **name**         | **description**     |
 |------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| `gene_token_id`  | gene identifiers corresponding to each gene with non-zero expression in each cell. to be used with `gene_expression`. <br> `metadata/gene_metadata.parquet` contains the mapping from  `gene_token_id` to Ensembl ID and official gene symbol |
-| `gene_expression`  | raw counts for each gene with non-zero expression. to be used with `gene_token_id`                                                                        |
+| `gene_token_id`  | gene identifiers corresponding to genes with non-zero expression in each cell. to be used with `gene_expression`. <br> `metadata/gene_metadata.parquet` contains the mapping from  `gene_token_id` to Ensembl ID and official gene symbol |
+| `gene_expression`  | raw counts for genes with non-zero expression. to be used with `gene_token_id`                                                                            |
 | `cell_barcode` | 10X-generated cell barcode. the suffix `-1` is replaced with `-<SAMPLE>`                                                                                      |
 | `sample`   | GEM batch                                                                                                                                                         |
 | `num_features`    | number of guides                                                                                                                                           |
@@ -55,7 +55,7 @@ The dataset contains the following information:
 | `total_counts`       | total UMIs                                                                                                                                              |
 | `total_counts_mt`      | total UMIs from MT genes                                                                                                                              |
 | `pct_counts_mt`      | % UMIs from MT genes                                                                                                                                    |
-| `pass_guide_filter`      | boolean if cells contains two guides from the same guide pair      |
+| `pass_guide_filter`      | boolean if cells contains two guides from the same guide pair                                                                                       |
 
 ## Gene metadata
 
@@ -68,9 +68,9 @@ gene_metadata = load_dataset("Xaira-Therapeutics/X-Atlas-Orion","gene_metadata")
 
 | name   | description                                                                                                 |
 |---------------|------------------------------------------------------------------------------------------------------|
-| `ensembl_id` | Ensembl ID                          |
-| `gene_name`  | official gene symbol    |
-| `gene_token_id`    | gene identifiers corresponding to each gene with non-zero expression in each cell. to be used with `gene_token_id` in the dataset |
+| `ensembl_id` | Ensembl ID                                                                                            |
+| `gene_name`  | official gene symbol                                                                                  |
+| `gene_token_id`    | gene identifiers corresponding to genes with non-zero expression in each cell. to be used with `gene_token_id` in the dataset |
 
 ## Citation
 ```