|
| Status |
Public on Sep 30, 2021 |
| Title |
kidney, sample 2, scATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
kidney paracancerous tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney
age: 55
Sex: female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Kidney paracancerous tissues was stored in PBS on ice and then cut into 1mm3 segments for nuclei isolation. Samples were homogenized using a Dounce homogenizer in 1ml chilled Lysis Buffer on ice. Following lysis, 9 ml chilled Wash Buffer was added and the resulting solution was filtered through a 30-µm cell strainer. Nuclei were centrifuged (500g for 5 min at 4 °C) and the supernatant removed without disrupting the nuclei pellet. Nuclei were resuspended in chilled Diluted Nuclei Buffer at approximately 3,000–4,000 nuclei per µl.
10X Chromium libraries were prepared according to manufacturer protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
peaks_and_bigwigs.tar
master_peak.bed
scATAC_SparseMatrix.rds
scATAC_barcodes.csv
|
| Data processing |
For each read, we first appended the barcode which was in the whitelist to the read name. Then adapter sequences were trimmed using trimmomatic (0.32). Bowtie2 (2.3.0) was used to align reads to the hg38 reference genome with ‘-X 2000 -3 1’ as options. Read pairs that did not map uniquely to autosomes or sex chromosomes with a mapping quality of at least 30 were filtered out using samtools (1.3.1).
High quality cells were identified as log10(unique fragments) > 3.4, ratio of fragments in TSS region > 0.15 and a log-transformed nucleosomal periodicity score > -1.75.
Harmony was used for batch correction and Louvain was used for clustering by SnapATAC package.
MACS2 was used for peak calling for each cluster with the following parameters:’ --nomodel --keep-dup all --extsize 200 --shift 100 –nolambda -q 0.001’. Peaks overlapping ENCODE blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists) were removed for each cluster to generate clean peaks and a master peak list was generated by taking clean peaks identified in any cluster and merged them with the bedtools.
Genome_build: hg38
Supplementary_files_format_and_content: bed file represents master peak list
Supplementary_files_format_and_content: csv file represents information of barcodes
Supplementary_files_format_and_content: tar file includes narrowpeaks and bigwig files for each cluster
Supplementary_files_format_and_content: rds Matrix table with raw counts for each peak in each cell
|
| |
|
| Submission date |
Feb 10, 2021 |
| Last update date |
Sep 30, 2021 |
| Contact name |
Jingping Yang |
| E-mail(s) |
jpyang@nju.edu.cn
|
| Organization name |
Nanjing University
|
| Department |
Medical School
|
| Street address |
22 Hankou Road
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210000 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE166547 |
Cell type-specific chromatin accessibility in kidney. |
|
| Relations |
| BioSample |
SAMN17860526 |
| SRA |
SRX10068562 |
