|
| Status |
Public on May 30, 2024 |
| Title |
Donor_7_Fetal_16w4d_NR_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
peripheral region of retina
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral region of retina
assay: 10x multiome-ATAC-v1
Sex: not determined
ethnicity: Unknown
age: 116 days (post-conception)
donor id: Donor_7
rawmatrix cellranger_assay_chemistry: SCMuv1
rawmatrix assays: snATAC-seq,snRNA-seq
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The human samples from PCW 10 to PCW 23 were collected from 12 individuals in this study from the UC Davis Eye Center. All the samples were collected within 6 hours post-mortem. The macula and peripheral retina samples were collected with a 2mm disposable biopsy punch and flash-frozen by liquid nitrogen. Samples were then stored at -80_C Nuclei were isolated by Wheaton Dounce Tissue Grinder in pre-chilled fresh-made RNase-free lysis buffer.
The snRNA-seq and snATAC-seq libraries were prepared with Chromium Next GEM Single Cell Multiome GEM kit (10x Genomics) following the manufacturer’s protocols.
scRNA-Seq, scATAC-Seq
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Multiome_16w4d_NR_filtered_feature_bc_matrix.h5
|
| Data processing |
The fastq files from the scRNA-seq and scATAC-seq libraries from each sample were processed into a single raw count matrix with both gene expression and ATAC peak counts using Cell Ranger arc v2.0.0. raw_matrix_normalized:False; raw_matrix_value_scale:linear; raw_matrix_feature_keys:gene symbol,genomic coordinates; raw_matrix_background_barcodes_included:False
Assembly: GRCh38
Supplementary files format and content: raw_matrix_file_format:hdf5; raw_matrix_value_units:UMI,fragment ends
Supplementary files format and content: fragments_file_format:tsv, fragments_file_content:per unique fragment information, fragments_file_tbi_content:fragment index
|
| |
|
| Submission date |
May 29, 2024 |
| Last update date |
May 30, 2024 |
| Contact name |
Lattice Data Coordination |
| E-mail(s) |
lattice-info@lists.stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Street address |
3165 Porter Drive
|
| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE265801 |
Single cell atlas of the human retina |
| GSE268630 |
Single Cell Multiome Atlas of the Human Fetal Retina |
|
| Relations |
| BioSample |
SAMN41593928 |
| SRA |
SRX24745442 |
