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| Status |
Public on Jul 26, 2024 |
| Title |
RPE, DCA+FGF 48h, 3 |
| Sample type |
SRA |
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| Source name |
RPE
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| Organism |
Gallus gallus |
| Characteristics |
tissue: RPE
treatment: Dichloroacetate + FGF2
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Explants were collected in 200 uL of DNA/RNA Shield buffer (Zymo Research, 1220-25). Total RNA was isolated using Quick-RNA Microprep Plus Kit Microprep (Zymo Research, R1051) following manufacturer’s instructions.
100ng of total intact RNA was used with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S), and the enriched mRNA was prepped for sequencing with the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (NEB, E7765S) per manufacturer’s instructions. A total of 13 PCR amplification cycles were used, and indexing was performed with single index oligos (NEB, 7710; NEB, 7730).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
Normalized_counts.tsv
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| Data processing |
Each sample was sequenced across two lanes of HiSeq X Ten. Raw fastq files for each sample were merged from the two lanes at the beginning of the analysis.
Adapters and low-quality bases were removed with Trim Galore v 0.6.4_dev with the parameters --stringency 3 --paired --length 36
A genome index for the STAR alignment software v2.7.5b was generated with the parameters --runMode genomeGenerate --sjdbOverhang 149 --genomeSAindexNbases 13, and splice sites were incorporated from Ensembl release 106
Trimmed reads were aligned to chicken genome GRCg6a using the STAR alignment tool and parameters --quantMode GeneCounts TranscriptomeSAM --runThreadN 30 --limitBAMsortRAM 60000000000 --readFilesCommand zcat --genomeLoad LoadAndKeep --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate
Gene counts were generated with Stringtie v2.1.4 using the parameters --rf -e
Count normalization was performed using DESeq2 v1.34.0
Assembly: GRCg6a
Supplementary files format and content: Normalized_counts.tsv contains tab-separated values of normalized gene counts generated by DESeq2 with default parameters. Rows represent genes based on the Ensembl annotation and each column is a unique biological sample.
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| Submission date |
Aug 04, 2022 |
| Last update date |
Jul 26, 2024 |
| Contact name |
Katia Del Rio-Tsonis |
| E-mail(s) |
delriok@miamioh.edu
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| Organization name |
Miami University
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| Department |
Biology
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| Street address |
700 E High St
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| City |
Oxford |
| State/province |
OH |
| ZIP/Postal code |
45056 |
| Country |
USA |
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| Platform ID |
GPL24517 |
| Series (1) |
| GSE210526 |
Metabolic activity affects RPE fate during cell reprogramming |
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| Relations |
| BioSample |
SAMN30150895 |
| SRA |
SRX16844814 |
| 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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