Result

Search results for the GEO ID: GSE35607

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GSM ID

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Title

Source name

Description

Characteristics

GSM871595

GPL1355

ETS Abnormal muscle fibers

Laser Capture microdissected muscle fibers from F344xBN F1 hybrid rat 36 month old

electron transport chain phenotype: Cytochrome C Oxidase negative, Succinate Dehydrogenase hyperreactive - ragged red tissue: Vastus lateralis skeletal muscle strain: F344 x BN F1 Hybrid rat age: 36 month old

Sample_geo_accession	GSM871595
Sample_status	Public on Mar 01 2013
Sample_submission_date	Feb 07 2012
Sample_last_update_date	Mar 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	cell isolation: Target Cells were isolated using an Arcturus PixCell II laser capture microscope. Captured cells and transfer film were further resected from LCM caps to minimize contamination
Sample_extract_protocol_ch1	RNA was isolated by using MagneSil total RNA mini-isolation kit, 30uL of Paramagnetic particles, 300ul Lysis buffer, DNASE I treatment
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA was eluted into 1st strand cDNA synthesis reaction primed with an anchored polyT-T7 promoter primer (5uM) Improm II cDNA synthesis system (Promega). First cycle second strand cDNA synthesis was performed and the entire reaction was used as template for T7 based RNA transcription using the T7 MegaScript High Yield Transcription kit (Ambion). The transcribed RNA was purified using the RNeasy mini kit (Qiagen). The nascent cRNA was subsequently subjected to a second cycle of first and second strand cDNA synthesis using random hexamer primers. The cDNA was cleaned up using the Wizard SV Gel and PCR cleanup kit (Promega) and the sample subjected to a second cycle of T7 RNA polymerase based amplification. In this final round of T7 based RNA transcription, biotinylated 14-CTP (Invitrogen) and 16-UTP (Roche) were incorporated into the transcription/labeling reaction. The labeled amplified cRNA was purified using the RNeasy mini kit and subsequently ethanol precipitated prior to A260 quantification and fragmentation.
Sample_hyb_protocol	Equal amounts of amplified cRNA, 7ug, from normal and abnormal muscle fibers was chemically fragmented and hybridized to the Affymetrix rat genome 230 2.0 high-density oligonuclotide arrays according to the manufacturers instructions (Affymetrix).
Sample_scan_protocol	Chips were scanned on an Affymetrix model 3000 array scanner
Sample_data_processing	GCOS v 1.40.036 was used to anaylyze the data. Genes that are called present/marginal from the ETS abnormal or control chips are considered specific to the population of cells from which they came and differentially expressed unless they are detected in both ETS and control samples. Additionally, genes whose expression is greater than a “two fold-change” are also considered to be differentially-regulated. Gene expression levels are not considered quantitative due to the inherent lack of normality derived from the small sample size and resulting amplification bias. Data was analyzed qualitatively. Genes detected from a given sample are considered differentially regulated as a result of their detection.
Sample_platform_id	GPL1355
Sample_contact_name	Allen,,Herbst
Sample_contact_institute	University of Alberta
Sample_contact_address	114C BARB
Sample_contact_city	Edmonton
Sample_contact_state	AB
Sample_contact_zip/postal_code	T6G 2R3
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM871nnn/GSM871595/suppl/GSM871595.CEL.gz
Sample_series_id	GSE35607
Sample_data_row_count	31099

GSM871596

GPL1355

Control Muscle Fibers

Laser Capture microdissected muscle fibers from F344xBN F1 hybrid rat 36 month old

electron transport chain phenotype: Cytochrome C Oxidase Positive, Succinate dehydrogenase Normal Muscle Fibers-Normal, Control tissue: Vastus lateralis skeletal muscle strain: F344 x BN F1 Hybrid rat age: 36 month old

Sample_geo_accession	GSM871596
Sample_status	Public on Mar 01 2013
Sample_submission_date	Feb 07 2012
Sample_last_update_date	Mar 01 2013
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	cell isolation: Target Cells were isolated using an Arcturus PixCell II laser capture microscope. Captured cells and transfer film were further resected from LCM caps to minimize contamination
Sample_extract_protocol_ch1	RNA was isolated by using MagneSil total RNA mini-isolation kit, 30uL of Paramagnetic particles, 300ul Lysis buffer, DNASE I treatment
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Total RNA was eluted into 1st strand cDNA synthesis reaction primed with an anchored polyT-T7 promoter primer (5uM) Improm II cDNA synthesis system (Promega). First cycle second strand cDNA synthesis was performed and the entire reaction was used as template for T7 based RNA transcription using the T7 MegaScript High Yield Transcription kit (Ambion). The transcribed RNA was purified using the RNeasy mini kit (Qiagen). The nascent cRNA was subsequently subjected to a second cycle of first and second strand cDNA synthesis using random hexamer primers. The cDNA was cleaned up using the Wizard SV Gel and PCR cleanup kit (Promega) and the sample subjected to a second cycle of T7 RNA polymerase based amplification. In this final round of T7 based RNA transcription, biotinylated 14-CTP (Invitrogen) and 16-UTP (Roche) were incorporated into the transcription/labeling reaction. The labeled amplified cRNA was purified using the RNeasy mini kit and subsequently ethanol precipitated prior to A260 quantification and fragmentation.
Sample_hyb_protocol	Equal amounts of amplified cRNA, 7ug, from normal and abnormal muscle fibers was chemically fragmented and hybridized to the Affymetrix rat genome 230 2.0 high-density oligonuclotide arrays according to the manufacturers instructions (Affymetrix).
Sample_scan_protocol	Chips were scanned on an Affymetrix model 3000 array scanner
Sample_data_processing	GCOS v 1.40.036 was used to anaylyze the data. Genes that are called present/marginal from the ETS abnormal or control chips are considered specific to the population of cells from which they came and differentially expressed unless they are detected in both ETS and control samples. Additionally, genes whose expression is greater than a “two fold-change” are also considered to be differentially-regulated. Gene expression levels are not considered quantitative due to the inherent lack of normality derived from the small sample size and resulting amplification bias. Data was analyzed qualitatively. Genes detected from a given sample are considered differentially regulated as a result of their detection.
Sample_platform_id	GPL1355
Sample_contact_name	Allen,,Herbst
Sample_contact_institute	University of Alberta
Sample_contact_address	114C BARB
Sample_contact_city	Edmonton
Sample_contact_state	AB
Sample_contact_zip/postal_code	T6G 2R3
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM871nnn/GSM871596/suppl/GSM871596.CEL.gz
Sample_series_id	GSE35607
Sample_data_row_count	31099

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