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| Status |
Public on Sep 30, 2022 |
| Title |
STAG3_SMC1B_RAD21L_c2: 3x RAD21L transgene clone 2 |
| Sample type |
SRA |
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| Source name |
colon epithelium
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| Organism |
Homo sapiens |
| Characteristics |
cell_line: immortalized tumor cells DLD-1
disease: colorectal adenocarcinoma
transgene: rtTA, Tet-On-STAG3, Tet-On-SMC1beta, and Tet-On-RAD21L lentiviruses
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| Treatment protocol |
For RNA-seq experiments, stable Tet-On transgenic DLD-1 cells and the control replicates were plated at 40% to 50% confluence in 10 cm plates, and induced by 200 ng/ml of doxycycline for 72 hours
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| Growth protocol |
DLD-1 cells and stably infected derivatives were grown in IMDM with 10% or 20% Tet-On certified FBS. Cells infected with lentivirus stock were selected for 4 weeks or more in media supplemented with 600µg/ml G418, 300 µg/ml zeocin, 1 µg/ml puromycin, or 200 µg/ml hygromycin B, dependent on the vector's marker, followed by the selection of individual clones.
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| Extracted molecule |
total RNA |
| Extraction protocol |
trizol, DNase I, oligo-dT beads enrichment, fragmentation with average size 200nt
cDNA libraries were prepared for sequencing using standard protocols, including: first strand synthesis using random hexamer primers, purification of dsDNA with magnetic beads, end repai, addition of single adenine to the 3' termini, sequencing adaptor ligation, and PCR amplification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Description |
infected with rtTA, Tet-On-STAG3, Tet-On-SMC1beta, and Tet-On-RAD21L lentiviruses
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| Data processing |
the original image data was transferred into sequence data via base calling, producing raw reads and saved as FASTQ files.
reads trimmed of adapters and low quality reads using Trim Galore v 0.5.0
clean FASTQ files generated.
gene counts calculated using RSEM v1.2.22, using rsem-calculate-expression with --bowtie2, --bowtie2-sensisitvity-level very_sensitive
reads aligned to hg38 assembly indexed with version 81 Ensembl GTF
pairwise differential expression values, PCA plots and MA plots generated using DESeq2 v1.24 in R v3.6.0.
Genome_build: hg38
Supplementary_files_format_and_content: (1) BigWig files from individual reads showing the RNA-seq signal genome-wide. (2) csv matrix DLD1_joined_RNA_expression.txt, with fields: ensg, gene_symbol, log2FoldChange, padj, and raw read counts.
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| Submission date |
Dec 18, 2019 |
| Last update date |
Oct 01, 2022 |
| Contact name |
Alexander V. Strunnikov |
| E-mail(s) |
alexstrunnikov@gmail.com
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| Organization name |
GIBH
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| Lab |
Molecular Epigenetics
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| Street address |
190 Kai Yuan Avenue
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510530 |
| Country |
China |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE142247 |
RNA-seq analysis of DLD-1 cell lines expressing cDNAs of subunits on human mei-cohesin complexes |
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| Relations |
| BioSample |
SAMN13620521 |
| SRA |
SRX7405729 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4223687_WHYR19053888_A_genome_sorted.bw |
5.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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