 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 29, 2024 |
| Title |
snATAC-Seq Hypothalamic Cells, rs7132908 AA, Differentiation 2, Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Hypothalamic cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Hypothalamic cells
genetic modification: rs7132908 G>A
Sex: Female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from each sample following 10X Genomics Chromium Single Cell Multiome ATAC + Gene Expression protocols
Libraries were prepared following the 10X Genomics Chromium Single Cell Multiome ATAC + Gene Expression workflow, according to manufacturer's instructions.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
AA2
|
| Data processing |
.fastq files were generated with Cell Ranger ARC version 2.0.2 -mkfastq
.fastq files were aligned to GRCh38 and cells were called using Cell Ranger ARC version 2.0.2 with parameters -count --min-atac-count=2000 --min-gex-count=1000
Cells underwent quality control with SoupX version 1.6.2, Scrublet version 0.2.3 and Seurat version 4.3.0
Samples were integrated with SCTransform version 0.3.5 and then Harmony version 0.1.1 was used for batch correction
Assembly: GRCh38
Supplementary files format and content: barcode.tsv contains 10X barcodes used to identify cells, features.tsv contains peak location, matrix.tx contains read counts for all cells
|
| |
|
| Submission date |
Aug 23, 2023 |
| Last update date |
Mar 29, 2024 |
| Contact name |
Sheridan Hope Littleton |
| E-mail(s) |
sl2225@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
Clinical Biochemistry
|
| Lab |
Giles Yeo
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0SL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE241593 |
Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3’ UTR of FAIM2 (snATAC-Seq) |
| GSE241691 |
Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3’ UTR of FAIM2 |
|
| Relations |
| BioSample |
SAMN37130026 |
| SRA |
SRX21475337 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
