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Sample GSM5061762 Query DataSets for GSM5061762
Status Public on Feb 04, 2021
Title rat-H3-METH-METH challenge-1 rep
Sample type genomic
 
Channel 1
Source name H3 hyperacetylation ChIP DNA from PFC METH-METH group
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
tissue: prefrontal cortex
gender: male
chip antibody: H3ac
Extracted molecule genomic DNA
Extraction protocol prefrontal cortex tissues were crosslinked with 1% formaldehyde at 37°C for 10 min, and then glycine was added to a final concentration of 0.125 M and incubated for 5 min to stop the crosslinking. Samples were centrifuged at 800 g at 4°C for 10 min to pellet tissues. The PFC tissues were sonicated on wet ice in 300 μl of nuclear lysis buffer using a sonicator (Sonics Vibra-cellTM, Sonics & Materials Inc., Newtown, Connecticut, USA). The sonication conditions were used: amplitude 70%, pulse 10 sec, and pause 59 sec for 9 cycles. The supernatant was collected as described in the instructions of a chromatin immunoprecipitation kit (Millipore, Cat. No. 17408). The lysate was precipitated with antibodies against acetyl-histone H3 (Millipore, Cat. No. 06599) and acetyl-histone H4 (Millipore, Cat. No. 06866).
Label Cy5
Label protocol 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
 
Channel 2
Source name Input DNA from PFC H3-METH-METH group
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
tissue: prefrontal cortex
gender: male
chip antibody: none, input DNA
Extracted molecule genomic DNA
Extraction protocol prefrontal cortex tissues were crosslinked with 1% formaldehyde at 37°C for 10 min, and then glycine was added to a final concentration of 0.125 M and incubated for 5 min to stop the crosslinking. Samples were centrifuged at 800 g at 4°C for 10 min to pellet tissues. The PFC tissues were sonicated on wet ice in 300 μl of nuclear lysis buffer using a sonicator (Sonics Vibra-cellTM, Sonics & Materials Inc., Newtown, Connecticut, USA). The sonication conditions were used: amplitude 70%, pulse 10 sec, and pause 59 sec for 9 cycles. The supernatant was collected as described in the instructions of a chromatin immunoprecipitation kit (Millipore, Cat. No. 17408). The lysate was precipitated with antibodies against acetyl-histone H3 (Millipore, Cat. No. 06599) and acetyl-histone H4 (Millipore, Cat. No. 06866).
Label Cy3
Label protocol 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).
 
 
Hybridization protocol The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)
Scan protocol Arrays were scanned on a NimbleGen MS 200 Microarray Scanner per manufacturer's protocol (http:// www.nimblegen.com/products/instruments/ under Literature).
Description Adult male Sprague-Dawley rats weighing 160-180 g were used in this study.
Data processing Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
 
Submission date Feb 03, 2021
Last update date Feb 04, 2021
Contact name Hui Li
E-mail(s) lihuiwzsszx@163.com
Organization name Beijing Key Laboratory of Neuropsychopharmacology
Street address 27th Taiping Road
City Beijing
ZIP/Postal code 100850
Country China
 
Platform ID GPL20661
Series (2)
GSE166095 Behavioral Sensitization Induced by Methamphetamine Causes Differential Alterations in Gene Expression and Histone Acetylation of the Prefrontal Cortex in Rats (Histone acetylation dataset)
GSE166096 Behavioral Sensitization Induced by Methamphetamine Causes Differential Alterations in Gene Expression and Histone Acetylation of the Prefrontal Cortex in Rats

Supplementary file Size Download File type/resource
GSM5061762_H3-METH-METH_group-IP.pair.gz 12.3 Mb (ftp)(http) PAIR
GSM5061762_H3-METH-METH_group-Input.pair.gz 12.4 Mb (ftp)(http) PAIR
Processed data are available on Series record

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