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Sample GSM979665 Query DataSets for GSM979665
Status Public on Aug 02, 2012
Title B2 Control rep2
Sample type SRA
 
Source name Hepa 1 WT cells
Organism Mus musculus
Characteristics cell type: Mouse Hepatoma
cell line: HC1C
treatment: untreated control
Treatment protocol Mouse Hepa cells were treated with vehicle control, FICZ (10 nM), or TA (50 uM) for 6 h.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNAeasy kit (QIAGEN, Valencia, CA). Samples were treated with de- oxyribonuclease (Invitrogen) before RNA quality control.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Base conversion was done using Illumina's OLB v1.9.
Mapping to mouse genome on Genomatix Mining Station with Genomatix Mapper version 3.5
Differential expression analysis on Genomatix GGA with RegionMiner program version 4.4 for transcript identification (Genomatix ElDorado database 08-2011) and DESeq (Anders & Huber, 2010) for assessment of differential expression.
Expression was summarized for genes where an annotated transcript was detected as differentially expressed with an adj. P-value < 0.05 (DESeq) and a log2fold - change >1 (uregulation) or < -1 (downregulation)
For assessment of Ahr induced gene expression only the profiles of upregulated genes were further used.
genome build: Mus musculus NCBI build 37
Supplementary_files_format_and_content: FB_result_transcript_summary.tsv: Mapping and contrast of FICZ treatment samples / Background samples to all transcripts in Genomatix' ElDorado annotation, raw counts, normalized expression, and evaluation of differential expression by DESeq Format description (1)
Supplementary_files_format_and_content: TB_result_transcript_summary.tsv: Mapping and contrast of Tryptamine treatment samples / Background samples to all transcripts in Genomatix' ElDorado annotation, raw counts, normalized expression, and evaluation of differential expression by DESeq Format description (1)
Supplementary_files_format_and_content: FT_result_transcript_summary.tsv: Contrast of FICZ treatment samples / Tryptamine samples to all transcripts in Genomatix' ElDorado annotation, raw counts, normalized expression, and evaluation of differential expression by DESeq Format description (1)
Supplementary_files_format_and_content: F_vs_B_up.txt: Differentially upregulated genes FICZ vs Background, summarized from the transcript data, adj. P - value < 0.05 (DESeq) and log2fold - change >1, Format description (2)
Supplementary_files_format_and_content: T_vs_B_up.txt: Differentially upregulated genes Tryptamine vs Background, summarized from the transcript data, adj. P - value < 0.05 (DESeq) and log2fold - change >1, Format description (2)
Supplementary_files_format_and_content: File Format(1) tab sparated text; Columns:
Supplementary_files_format_and_content: 1: accession number of the transcript (e.g. RefSeq, Genbank, Ensembl)
Supplementary_files_format_and_content: 2: symbol of the gene
Supplementary_files_format_and_content: 3: gene ID (NCBI Entrez Gene, 0 if not available, -2 if ambiguous)
Supplementary_files_format_and_content: 4: length of the transcript (sum of exons)
Supplementary_files_format_and_content: 5: number of exons
Supplementary_files_format_and_content: 6: p-value (DESeq)
Supplementary_files_format_and_content: 7: adjusted p-value (Benjamini - Hochberg)
Supplementary_files_format_and_content: 8: log2(fold change), i.e. log2(expression value of control data set / expression value of treatment data set), note, that this value can be -Inf/+Inf if one of the conditions shows no expression
Supplementary_files_format_and_content: 9: Regulation of treatment (set1) compared to control (set2), (values can be "up", "down", "no")
Supplementary_files_format_and_content: 10, 11, 12: number of reads for each replicate from the treatment set
Supplementary_files_format_and_content: 13, 14, 15: number of reads for each replicate from the control set
Supplementary_files_format_and_content: 16, 17, 18: normalized expression value for each replicate from the treatment set
Supplementary_files_format_and_content: 19, 20, 21: normalized expression value for each replicate from the control set
Supplementary_files_format_and_content: 22: the mean normalized expression value across the treatment replicates
Supplementary_files_format_and_content: 23: the standard deviation of the normalized expression values across the treatment replicates
Supplementary_files_format_and_content: 24: the mean normalized expression value across the control replicates
Supplementary_files_format_and_content: 25: the standard deviation of the normalized expression values across the control replicates
Supplementary_files_format_and_content: File Format(2) tab sparated text; Columns:
Supplementary_files_format_and_content: 1: gene ID (NCBI Entrez Gene)
Supplementary_files_format_and_content: 2: symbol of the gene
Supplementary_files_format_and_content: 3: number of alternative transcripts for this gene that are up-/down-regulated regulated
Supplementary_files_format_and_content: 4: total number of alternative transcripts for this gene
Supplementary_files_format_and_content: 5: mean log2 fold change of up-/down-regulated transcripts
Supplementary_files_format_and_content: 6: min log2 fold change of up-/down-regulated transcripts
Supplementary_files_format_and_content: 7: max log2 fold change of up-/down-regulated transcripts
Supplementary_files_format_and_content: 8: standard deviation across the log2 fold change values of the alternative transcripts
Supplementary_files_format_and_content: 9: minimum p_value for the alternative transcripts
Supplementary_files_format_and_content: 10: mean NE(treat): mean normalized expression value for the alternative transcripts in the treatment data
Supplementary_files_format_and_content: 11: stddev NE(treat): standard deviation across the NE values for the alternative transcripts in the treatment data
Supplementary_files_format_and_content: 12: mean NE(ctrl): mean normalized expression value for the alternative transcripts in the control data
Supplementary_files_format_and_content: 13: stddev NE(ctrl): standard deviation across the NE values for the alternative transcripts in the control data
Supplementary_files_format_and_content: Normalized expression/enrichment value (NE-value) The NE-value is calculated based on the following formula: NE = c * #readsregion / (#readsmapped * lengthregion) where NE is the normalized expression or enrichment value, #readsregion: the reads (sum of base pairs) of falling into either the transcript or the cluster region, #readsmapped: all mapped reads (in base pairs), lengthregion: the transcript or cluster length in base pairs and c a normalization constant set to 10E7. Except for the constant this is equivalent to RPKM
 
Submission date Aug 01, 2012
Last update date May 15, 2019
Contact name Bernward Klocke
E-mail(s) klocke@genomatix.de
Organization name Genomatix Software GmbH
Street address Bayerstr. 85a
City Munich
ZIP/Postal code D-80335
Country Germany
 
Platform ID GPL13112
Series (1)
GSE39812 Tryptamine Serves As a Proligand of the AhR Transcriptional Pathway, and the Activation Is Dependent of Monoamine Oxidases
Relations
SRA SRX172600
BioSample SAMN01096360

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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