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| Status |
Public on Jun 28, 2021 |
| Title |
E15.5 Scx-RNAseq control2 |
| Sample type |
SRA |
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| Source name |
GFP+ forelimb cells
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| Organism |
Mus musculus |
| Characteristics |
age: E15.5
antibody: no
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| Extracted molecule |
total RNA |
| Extraction protocol |
E15.5 forelimb samples were freshly dissected,digested with trypsin-EDTA solution at 37°C for 4 minutes. After inactivation of trypsin with DMEM containing 10% FBS, cells were dissociated by pipetting. The dissociated cells were resuspended in PBS with 2% FBS and 10 mM EDTA, and filtered through a 40 μm nylon cell strainer, GFP+ cells were isolated using BD FACSAria II. RNA was extracted by Qiagen RNeasy Micro kit.
Sequencing libraries were generated by using Illumina Nextera DNA Sample Prep kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
RNAseq-Ctrl_vs_Null
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| Data processing |
RNA-seq reads were aligned as described in ChIP-seq data analysis. Read counts for each genes were measured using featureCount in subread packcage (ver. 1.6.2) [4]. To avoid sex-specific bias in the analysis, genes in chrY were discarded. Also, we used RUVseq (RUVs, k=1) [5] to account for sex-specific contribution to the gene expression profiles and to identify sex-independent gene expression changes upon Scx deletion. Differential gene expression analysis was performed using DESeq2 [6]. Differentially expressed genes were identified by FDR < 0.05. Gene ontology analysis was performed using EnrichR [7]. Hierarchical clustering was performed using the differential genes using 1 – Pearson correlation coefficient of log-transformed gene expression level (FPKM) as a dissimilarity measure under Ward’s criterion. Clustering heatmap was visualized in z-score.
mm10
excel file, list of all transcription entities
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| Submission date |
Apr 27, 2021 |
| Last update date |
Jun 28, 2021 |
| Contact name |
HAN LIU |
| E-mail(s) |
han.liu@cchmc.org
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| Organization name |
CINCINNATI CHILDREN'S HOSPITAL
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| Department |
DEVELOPMENTAL BIOLOGY
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| Lab |
Jiang
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| Street address |
3333 burnet avenue
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| City |
cincinnati |
| State/province |
oh |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE173428 |
Genome-wide identification of Scx transcriptional target genes in tendon development II |
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| Relations |
| BioSample |
SAMN18880113 |
| SRA |
SRX10687855 |
| 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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