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| Status |
Public on Dec 16, 2019 |
| Title |
AACG4 |
| Sample type |
SRA |
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| Source name |
Human trabecular meshwork tissue
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| Organism |
Homo sapiens |
| Characteristics |
subject source: acute angle-closure glaucoma
tissue/cell type: Human trabecular meshwork (HTM) tissue
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted by the hot phenol method. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1.5μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
tisssue of patient with glaucoma
AACG4-mRNA_raw
processed data file: clin_expressed_gene_*.txt
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| Data processing |
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2 Pvalue <= 0.01 Qvalue < =0.05
Genome_build: GRCH38
Supplementary_files_format_and_content: txt; abundance measurements
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| Submission date |
Nov 29, 2018 |
| Last update date |
Dec 16, 2019 |
| Contact name |
Dong Chen |
| Organization name |
ABLife, Inc.
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| Department |
Center for Genome Analysis
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| Street address |
388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430075 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE123100 |
Transcriptome-wide study of the response of human trabecular meshwork cells to the substrate stiffness increase |
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| Relations |
| BioSample |
SAMN10497146 |
| SRA |
SRX5077372 |
| 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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