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| Status |
Public on Nov 05, 2020 |
| Title |
XD456 DMSO 12H; second experiment |
| Sample type |
SRA |
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| Source name |
PDGx cell line XD456
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| Organism |
Homo sapiens |
| Characteristics |
subtype: proneural subtype
tissue: GBM, brain tumor
treatment: treated with DMSO, 0.012%
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| Treatment protocol |
Neurospheres were treated in the growth media with SRI-42127 (3uM for 12 hours) or with the corresponding concentration of DMSO (0.012% for 12 hours), as the control.
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| Growth protocol |
The neurospheres were formed and maintained in Neurobasal-A medium (Gibco, Carlsbad, CA, USA) supplemented with a B27 supplement without vitamin A (Gibco), N-2 supplement (Gibco), 2mM L-Glutamine (Media tech, Inc., Manassas, VA, USA), the basal growth factors (EGF, 20 ng/ml and bFGF, 20 ng/ml, were both purchased from Termo Fisher Scientifics (Grand Island, NY, USA)), and 100 U/ml Penicillin/Streptomycin (Media tech, Inc., Manassas, VA, USA).
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by using the standard protocol for RNA isolation by using TRIzol Reagent (Invitrogen, Carlsbad, CA). Briefly, neurospheres were collected in growth media, spin down for 5 min at 900 rpm (136 g), neurosphere pellet was washed in PBS, spin down for 5 min at 900 rpm, and the fully aspirated pellet was resuspended in TRIzol Reagent. After RNA purification, the RNA concentration and purity were evaluated by using NanoDrop 1000. The RNA samples were processed, and the sequencing libraries were prepared from RNA samples, which had integrity number higher than 7.0, in the UAB Sequencing Core facility.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
second experiment
SY5
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| Data processing |
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Sequence reads were aligned to the reference genome using STAR version 2.7.2a with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using HTSeq-Count version 0.11.1 with paramaters -r pos; -t exon; -i gene_id; -a 10; -s no; -f bam
Normalization and pairwise differential expression was calculated following the DESeq2 vignette
Genome_build: Gencode GRCh38 p7 Release 25
Supplementary_files_format_and_content: tab-delimited Excel file containing raw counts for each gene in each sample
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| Submission date |
Sep 21, 2020 |
| Last update date |
Nov 05, 2020 |
| Contact name |
Louis Burt Nabors |
| E-mail(s) |
bnabors@uab.edu
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| Phone |
2059341432
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| Organization name |
University of Alabama at Birmingham
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| Department |
Neurology
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| Lab |
Neuro-oncology Lab
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| Street address |
510 20th Street South, FOT 1020
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| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE158271 |
Targeting the HuR oncogenic role with a new class of inhibitors of HuR dimerization |
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| Relations |
| BioSample |
SAMN16230164 |
| SRA |
SRX9162339 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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