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Sample GSM979671

Query DataSets for GSM979671

Status

Public on Aug 02, 2012

Title

T2 Tryptamin treated rep2

Sample type

SRA

Source name

Hepa 1 WT cells

Organism

Mus musculus

Characteristics

cell type: Mouse Hepatoma
cell line: HC1C
treatment: TA (50 uM) for 6 h

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