|
| Status |
Public on Oct 27, 2024 |
| Title |
Central lens epithelial cells, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
lens
|
| Organism |
Homo sapiens |
| Characteristics |
hours_post_injury: 0
cell_type: central_epithelium
donor: 2
lens: a
date_of_capsulotomy: 17-Apr-2019
date_cells_transferred_to_rna_later: 17-Apr-2019
age_years: 79
Sex: F
post_mortem_hours_before_sample_prep: 5h
cause_of_death: Pancreatic_cancer
|
| Treatment protocol |
Ex-vivo micro
|
| Growth protocol |
24 Hour injury samples were cultured under the following conditions: capsular bag was cultured in medium (RPMI-1640 with 5% fetal calf serum (FCS), 1% 10,000 units penicillin, 10 mg and 25 mg amphotericin B per mL for 24 hours. streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy Kit
SMARTer Stranded Total RNA-Seq kit v2-Pico Input Mammalian
Primer directed ribosomal depletion
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
HPS1_Capsule_vs_Rhexis_Pairwise_Exact_Test_Differential_Expression.xlsx
HPS1_Fibers_vs_Rhexis_Pairwise_Exact_Test_Differential_Expression.xlsx
|
| Data processing |
Trimmed for quality and adapter content with Trim Galore! Version 0.6.6 Call: trim_galore -o $TRIMDIR --length 85 --paired --clip_R2 3 --phred33 --cores 8
Aligned to RN45S5 transcript to reduce ribosomal content using HISAT2 2.2.1: hisat2 -p8 --verbose --phred33 --dta --fr
Convert rRNA Alignments to BAM samtools 1.9/htslib 1.9: samtools view -@ 8 -bS
sort rRNA Alignments samtools 1.9/htslib 1.9:samtools sort -n -@ 8 -m 12G
Extracted reads that don't align to RN45S5 using bedtools v2.29.2: bedtools bamtofastq
Aligned non-ribosomal reads to Human Genome using HISAT2 2.2.1: hisat2 -p8 --verbose --phred33 --dta --fr --rna-strandness RF
Counted reads aligning to genomic features in the Ensembl v104 GTF File using HTSeq Count 0.13.5: htseq-count -i gene_id -r pos -f bam -s reverse -m union --type exon
Assembled a DGEList object from all study samples, edgeR version 3.34.1
For each pairwise contrast, extracted a subset dgelist containing only samples participating in that contrast
Filtered low counts using edgeR's filterByExpr with default settings for each contrast. edgeR version 3.34.1
Calculated TMM scaling factors edgeR's calcNormFactors with default settings, for each contrast. edgeR version 3.34.1
Estimated robust dispersions for each contrast using "estimateDisp(dgelist, robust=TRUE)". edgeR version 3.34.1
Analyzed differential gene expression in each pairwise contrastusing edgeR's exact test. edgeR version 3.34.1
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: The processed data files are excel workbooks that contain the raw count matrix for the target contrast (all features in the GTF File) and tables of differential expression statistics.
|
| |
|
| Submission date |
Oct 27, 2021 |
| Last update date |
Oct 27, 2024 |
| Contact name |
Melinda K. Duncan |
| E-mail(s) |
duncanm@udel.edu
|
| Phone |
3028310533
|
| Organization name |
University of Delaware
|
| Department |
Biological Sciences
|
| Lab |
Vertebrate Development
|
| Street address |
327 Wolf Hall
|
| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19716 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE186716 |
Injury response of human lens epithelial cells ex-vivo |
|
| Relations |
| BioSample |
SAMN22608570 |
| SRA |
SRX12800916 |
