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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 02, 2023 |
| Title |
D2_TGFb_3 |
| Sample type |
SRA |
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| Source name |
cornea
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| Organism |
Felis catus |
| Characteristics |
tissue: cornea
cell type: fibroblast
treatment: TGFb1 (1ng/ml) biological replicate 3
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA) per manufacturers recommendations. RNA concentration was determined with the NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA).
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina flow cell and sequenced using the NovaSeq6000 sequencer (Illumina, San Diego, CA) SP flow cell.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
As above, following two days of treatment with TFGb1
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| Data processing |
Data Formatting bcltofastq-2.19.1
Data Cleaning fastp 0.23.1, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment STAR_2.7.9a, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1 subread-2.0.1, featurecounts, -s 2 -t exon -g gene_name
Read Quantification3 salmon-1.5.2, --seqBias --gcBias --posBias
Assembly: Felis Catus 9.0, ensemble release 108
Supplementary files format and content: gene counts
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| Submission date |
May 05, 2023 |
| Last update date |
Nov 02, 2023 |
| Contact name |
Tyler Stahl |
| Organization name |
University of Rochester Medical Center School of Medicine and Dentistry
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| Street address |
601 Elmwood Ave
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| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
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| Platform ID |
GPL28702 |
| Series (1) |
| GSE231796 |
Mitochondria as key therapeutic targets for the treatment of corneal fibrosis |
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| Relations |
| BioSample |
SAMN34720336 |
| SRA |
SRX20235780 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7300488_D2_TGFb_3_countsU.txt.gz |
71.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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