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Sample GSM6431935 Query DataSets for GSM6431935
Status Public on Jul 26, 2024
Title RPE, FGF 24h, 1
Sample type SRA
 
Source name RPE
Organism Gallus gallus
Characteristics tissue: RPE
treatment: FGF2
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description Normalized_counts.tsv
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.
 
Submission date Aug 04, 2022
Last update date Jul 26, 2024
Contact name Katia Del Rio-Tsonis
E-mail(s) delriok@miamioh.edu
Organization name Miami University
Department Biology
Street address 700 E High St
City Oxford
State/province OH
ZIP/Postal code 45056
Country USA
 
Platform ID GPL24517
Series (1)
GSE210526 Metabolic activity affects RPE fate during cell reprogramming
Relations
BioSample SAMN30150912
SRA SRX16844797

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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