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| Status |
Public on Sep 14, 2023 |
| Title |
Pre-transplant, future_aGVHD, rep1 |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMC
group: Pre-transplant, future_aGVHD
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were removed from liquid nitrogen and thawed in aMEM supplemented with 10% FBS and a DNASe-containing dextran-Albumin solution. We utilized a bead based magnetic separation approach to isolate live cells.
Viable cells were counted and then scATAC libraries were prepared using the 10x Chromium Chromium Next GEM Single Cell ATAC Kit v2 (cat # 1000406). These ATAC libraries were technically single index, but were sequenced in a dual index format (50x8x16x50) and were sequenced at a depth of 25-50,000 read pairs per cell on either the Illumina NextSeq2000P2 or Illumina NovaSeq SP.
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| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Tn5 cut DNA
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0.0. Addiitonal analyses were performed using Seruat v.4.3.0.
Assembly: hg38
Supplementary files format and content: h5 (count matrix), ATAC fragment file, fragment index file, bed file (cellRanger_atac_peakcalls), csv file (cellRanger_per_barcode_info).
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| Submission date |
May 08, 2023 |
| Last update date |
May 30, 2024 |
| Contact name |
SONIA LAURIE |
| E-mail(s) |
sonia.laurie@gmail.com
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| Organization name |
UNC CHAPEL HILL
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| Street address |
125 Mason Farm Road
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| City |
CHAPEL HILL |
| State/province |
NC |
| ZIP/Postal code |
27514 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE232002 |
Multiomic Single Cell Evaluation Reveals Inflammatory Cytokines Affect Innate Lymphoid Cell Fate After Allogeneic Stem Cell Transplantation [scATAC-Seq] |
| GSE232003 |
Multiomic Single Cell Evaluation Reveals Inflammatory Cytokines Affect Innate Lymphoid Cell Fate After Allogeneic Stem Cell Transplantation |
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| Relations |
| BioSample |
SAMN35004344 |
| SRA |
SRX20260815 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7308372_Exp157DukeaBMTF_filtered_peak_bc_matrix.h5 |
37.5 Mb |
(ftp)(http) |
H5 |
| GSM7308372_sampleF_fragments.tsv.gz |
841.5 Mb |
(ftp)(http) |
TSV |
| GSM7308372_sampleF_fragments.tsv.gz.tbi.gz |
711.7 Kb |
(ftp)(http) |
TBI |
| GSM7308372_sampleF_peaks.bed.gz |
771.0 Kb |
(ftp)(http) |
BED |
| GSM7308372_sampleF_singlecell.csv.gz |
3.0 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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