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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 30, 2016 |
| Title |
24h RN TCDD |
| Sample type |
SRA |
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| Source name |
primary B cell
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
Sex: Female
age: 6-9 weeks
treatment: TCDD
concentration: 30
concentration unit: nM
duration: 24
duration unit: hours
replicate: 1
activation method: pokeweed mitogen
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| Treatment protocol |
Isolated priary cells were activated with 15 ug/ml pokeweed mitogen (PWM) and treated with either vehicle (0.02%) DMSO or 30 nM TCDD and incubated for 4, 8 and 24h.
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| Growth protocol |
Primary mouse and rat B cells were isolated from spleens (female mice and rats 6-9 weeks old) using Miltenyi untouched Mouse/Rat B cell isolation kit. Primary human B cells were isolated from leukopaks donated by anonymous female donors using Miltenyi naive human B cell isolation kit. After isolation cells were cultured in RPMI1640 medium supplemented with 10% serum.
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| Extracted molecule |
total RNA |
| Extraction protocol |
B cells vere collected 4, 8 and 24h pot-treatment, preserved in RNA later stabilization reagent QIAGEN , and RNA was harvested using RNeasy Plus Mini kit (QIAGEN) according to manufacturer's instructions. RNA was quantified and examined for purity and quality by nanodrop, Qubit and Bioanalyzer. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were were prepared using the Illumina TrueSeq RNA sample preparation kit according to manufacturers instructions. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
FASTQC v0.11.2 was used for quality control
FASTX v0.0.14 and Cutadapt 1.4.1 was used for adaptor removal and removal of low-complexity reads
TopHat v1.4.1 was used for alignment
SAMTools v0.1.19 was used for file conversion
HTSeq v0.6.1 was used to count feature aligned reads
DESeq was used to transform counts
Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 81 (mouse), Rn5 release 76 (rat), GRch38 release 76 (human)
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene
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| Submission date |
Apr 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Norb Kaminski |
| E-mail(s) |
[email protected]
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| Phone |
5175289884
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| Organization name |
MSU
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| Street address |
1129 Farm Ln, rm. 248
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| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE80953 |
Temporal comparison of transcriptomic alterations in human, mouse and rat primary B lymphocytes exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) |
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| Relations |
| BioSample |
SAMN04916696 |
| SRA |
SRX1737121 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2138933_24h_TCDD_r_count.txt.gz |
99.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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