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Status |
Public on Jul 26, 2024 |
Title |
RPE, DCA+FGF 24h, 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 |
SAMN30150907 |
SRA |
SRX16844802 |
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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