|
| Status |
Public on Feb 15, 2024 |
| Title |
Pooled SHARE-seq sublibraries from human kidney tissues (ATAC-seq Novaseq S4 2nd run) |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei isolation from human kidney tissues
An optimized SHARE-seq protocol
snRNA-seq and snATAC-seq in the same cells
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
snATAC-seq, paired with Novaseq_S4_2_RNA
|
| Data processing |
bowtie2 (ATAC) or STAR (RNA) alignment
demultiplexing with customized scripts
duplicate removal with Picard
read annotation with featurecounts
UMI-Tools for matrix creation (Overall, using codes from either https://github.com/masai1116/SHARE-seq-alignment or https://github.com/masai1116/SHARE-seq-alignmentV2/
Assembly: hg19
Supplementary files format and content: h5 or h5ad file: count matrix for snRNA-seq
Supplementary files format and content: csv.gz file: cell-by-gene count matrix for snRNA-seq
Supplementary files format and content: bed.gz or tsv.gz file: fragment profile for snATAC-seq
Supplementary files format and content: Two extra supp files (primer_sequence.py, P5_primer_ID.txt). They clarify the barcode sequences and the specific P5 primers of use. Users should be able to perform all analysis with this information.
|
| |
|
| Submission date |
Jun 13, 2023 |
| Last update date |
Feb 15, 2024 |
| Contact name |
Benjamin Humphreys |
| Organization name |
Washington University School of Medicine
|
| Street address |
660 S Euclid Ave
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE234788 |
Single-cell multiome sequencing of human kidney anatomical regions with SHARE-seq |
|
| Relations |
| BioSample |
SAMN35724154 |
| SRA |
SRX20669591 |
