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| Status |
Public on Nov 07, 2022 |
| Title |
pNF-2-006 |
| Sample type |
SRA |
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| Source name |
Peripheral nerve tumor
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| Organism |
Homo sapiens |
| Characteristics |
tissue: plexiform neurofibroma
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| Extracted molecule |
total RNA |
| Extraction protocol |
For human patient samples, tumor tissues were resected by surgery, cut into pieces of up to 2 mm and cryopreserved in 10% DMSO in liq N2. Tissues requested were shipped and transported to Lu lab in dry ice from Johns Hopkins NF repository. For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM Medium+ 2 mg/ml of collagenase IV), and single cells were processed through the 10X Chromium 3' Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol. Briefly, up to 16,000 cells were loaded to each channel of a chip to be partitioned into Gel Beads in Emulsion (GEMs) in the Chromium instrument, followed by cell lysis and barcoded reverse transcription of RNA in the droplets. Breaking of the emulsion was followed by amplification, fragmentation and addition of adapter and sample index. The libraries were pooled and sequenced on NovaSeq 6000 (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
For 10X Genomics data, CellRanger was used for base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: hg19
Supplementary_files_format_and_content: CellRanger output files
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| Submission date |
Jun 28, 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) |
| GSE179033 |
Transcriptional programs dictating Schwann cell transformation in MPNST [10X scRNA-seq] |
| GSE179043 |
Transcriptional programs dictating Schwann cell transformation in MPNST |
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| Relations |
| BioSample |
SAMN19919140 |
| SRA |
SRX11243100 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5404034_NF-2-006-filtered_feature_bc_matrix.tar.gz |
55.4 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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