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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 07, 2022 |
| Title |
MPNST_2-084 |
| Sample type |
SRA |
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| Source name |
Peripheral nerve tumor
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| Organism |
Homo sapiens |
| Characteristics |
tissue: MPNST
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nerve tumors were dissociated into single cells suspensions using digestion buffer (DMEM Medium+ 2 mg/ml of collagenase IV). Cells were washed in 1x PBS and red blood cells were lysed using RBC lysis buffer (Roche) for 10 minutes at room temperature. Cells were filtered using a 40um strainer followed by lysis in Nuclei EZ buffer for 3-5 min. 1 ml nuclei wash buffer was pipetted into lysed nuclei, which were then centrifuged for 5 min at 500 x g. Nuclei were resuspended at appropriate concentration for scATACseq in Nuclei Buffer supplied by 10X Genomics.
single-cell libraries were generated using the GemCode Single-cell instruments and the Single Cell ATAC Library & Gel Bead Kit and ChIP Kit from 10x Genomics, according to the manufacturer’s instructions. The samples were incubated at 37°C for 1 h with 10 μl of transposition mix (per reaction, 7 μl ATAC Buffer, and 3 μl ATAC Enzyme (10x Genomics)). Following the generation of nanoliter-scale Gel bead-in-EMulsions (GEMs), GEMs were reverse transcribed in a C1000 Touch Thermal Cycler (Bio-Rad) programmed at 72°C for 5 min, 98°C for 30 s, 12 cycles of 98°C for 10 s, 59°C for 30 s, and 72°C for 1 min, and held at 15°C. After reverse transcription, single-cell droplets were broken and the single-strand cDNA was isolated, cleaned up and amplified. Amplified cDNA and final libraries were assessed on an Agilent BioAnalyzer using a High Sensitivity DNA Kit (Agilent Technologies) at the Gene Expression Core at CCHMC. The libraries were pooled and sequenced on NovaSeq 6000 (Illumina) at a depth of approximately 400M reads per sample at the DNA Sequencing Core at CCHMC.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
For 10X genomics datasets, we used Cellranger v5.0.1 to align reads to the mm10 or hg19 human reference sequence.
Genome_build: mm10 for mouse; hg19 for human
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| Submission date |
Jun 27, 2021 |
| Last update date |
Nov 07, 2022 |
| Contact name |
Lai Man (Natalie) Wu |
| E-mail(s) |
laiman.wu@cchmc.org
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| Organization name |
CCHMC
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| Street address |
3333 Burnet Avenue, MLC7013,Lu lab, T6.525
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| City |
CINCINNATI |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE178988 |
Transcriptional programs dictating Schwann cell transformation in MPNST [scATACseq] |
| GSE179043 |
Transcriptional programs dictating Schwann cell transformation in MPNST |
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| Relations |
| BioSample |
SAMN19904574 |
| SRA |
SRX11238022 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5402772_MPNST_2-084_filtered_peak_bc_matrix.h5 |
34.9 Mb |
(ftp)(http) |
H5 |
| GSM5402772_MPNST_2-084_fragments.tsv.gz |
1.4 Gb |
(ftp)(http) |
TSV |
| GSM5402772_MPNST_2-084_fragments.tsv.gz.tbi.gz |
894.3 Kb |
(ftp)(http) |
TBI |
| GSM5402772_MPNST_2-084_singlecell.csv.gz |
7.1 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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