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| Status |
Public on Sep 11, 2023 |
| Title |
KD_3 |
| Sample type |
SRA |
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| Source name |
Sciatic nerve
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Sciatic nerve
cell type: Primary cultured Schwann cells
condition: differentiation
genotype: WT
treatment: Stat1 siRNA
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| Treatment protocol |
SCs were seeded at a density of 3 × 10^6 cells/ml in 24-well plates and cultured for 24 h, after which they were transfected with Stat1-siRNAs and non-targeting negative control (Scramble). 48 hours after transfection, the cells were cultured in differentiation medium containing DMEM/F12 (11320-033, Gibco) plus 1% FBS, 1 mM dibutyryl cyclic AMP (db-cAMP; D0627, Sigma) and 20 ng/ml Nrg1 for 3 d to acquire a differentiated phenotype.
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| Growth protocol |
Schwann cells (SCs) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 5 μM forskolin, 2 ng/ml Nrg1 and 1x penicillin/streptomycin, and cultured in humidified atmosphere with 5% CO2 at 37ºC.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol (15596-018-056, Thermo Fisher, Cleveland, OH, USA) followed by purification using RNeasy Mini Kit (Qiagen, Valencia, CA, USA). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.
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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 |
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence/containing poly-N sequence using CLC genomic benchwork (parameter- Quality limit: 0.05).
Trimmed sequence reads were mapped to the reference UCSC genome (RGSC6.0/rn6) using Hisat2 v2.0.5.
Read count extraction and normalization were performed using FeatureCounts v1.5.0-p3.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: rn6
Supplementary files format and content: all compare.txt: Tab-delimited text file includes counts and FPKM values for each Sample.
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| Submission date |
Aug 15, 2022 |
| Last update date |
Sep 11, 2023 |
| Contact name |
Yun Gu |
| E-mail(s) |
guyun@ntu.edu.cn
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| Organization name |
Nantong University
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| Street address |
19 Qixiu Road
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| City |
Nantong |
| State/province |
Jiangsu |
| ZIP/Postal code |
226001 |
| Country |
China |
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| Platform ID |
GPL25947 |
| Series (2) |
| GSE211336 |
The transcription factor Stat-1 is essential for Schwann cell differentiation, myelination and myelin sheath regeneration [RNA-seq] |
| GSE211338 |
The transcription factor Stat-1 is essential for Schwann cell differentiation, myelination and myelin sheath regeneration |
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| Relations |
| BioSample |
SAMN30327917 |
| SRA |
SRX17087994 |
| 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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