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| Status |
Public on Apr 07, 2020 |
| Title |
Day_0_FSHD2_2_R1_G5 |
| Sample type |
SRA |
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| Source name |
Primary myoblasts
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| Organism |
Homo sapiens |
| Characteristics |
individual: FSHD2-2
day of differentiation: Day 0
fshd status: FSHD2
cell or nucleus: cell
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Day 0 myoblasts were lifted from plates using trypsin, washed, and captured on medium IFCs (10-17 um). Day 3 myotube single nuclei were isolated from mononucleated cells (MNCs) by washing a 6 cm dish once with trypsin, then adding trypsin for about 5 min until myotubes lifted off the plate and MNCs were still attached. Cells were initially pelleted at 2000 rpm for 2 min and resuspended in lysis buffer with 0.02% IGEPAL CA-630. Lysis was done for 3 minutes, filtered and spun at 4000 rpm for 1 minute. Nuclei were captured on medium IFCs (10-17 um) at a density between 340 and 640 nuclei/ul in a volume of 10 ul.
cDNA was normalized to approximately 0.1 ng/ul for tagmentation and library prep (Illumina, FC-131-1096). Libraries were sequenced on the Illumina NextSeq500 platform using paired-end 75 bp mode with 1-3 million reads per sample for full length RNA-seq single-cell and single-nucleus libraries.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
poly-A+ RNA
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| Data processing |
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Reads were mapped to hg38 by STAR (version 2.5.1b) using defaults except with a maximum of 10 mismatches per pair, a ratio of mismatches to read length of 0.07, and a maximum of 10 multiple alignments.
Quantitation was performed using RSEM (version 1.2.31) by defaults with gene annotations from GENCODE v28, and results were output in transcripts per million (TPM).
Genome_build: hg38
Supplementary_files_format_and_content: RSEM output tab-delimited text files with abundance measures in counts and TPM
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| Submission date |
Jan 12, 2020 |
| Last update date |
Apr 08, 2020 |
| Contact name |
Ali Mortazavi |
| E-mail(s) |
ali.mortazavi@uci.edu
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| Organization name |
UC Irvine
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| Street address |
2300E Biological Sciences 3
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| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE143492 |
Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei [Fluidigm] |
| GSE143493 |
Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei |
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| Relations |
| BioSample |
SAMN13830921 |
| SRA |
SRX7544281 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4260528_Day_0_FSHD2_2_R1_G5_rsem_hg38.genes.results.txt.gz |
756.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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