|
| Status |
Public on Dec 26, 2007 |
| Title |
Mammary_biopsy_control_pooled (SAGE) |
| Sample type |
SAGE |
| Anchor |
NlaIII
|
| Tag Count |
7318 |
| Tag Length |
10 |
| |
|
| Source name |
biopsy of mammary parenchyma, milked twice daily, approx. day 7 of lactation
|
| Organism |
Bos taurus |
| Characteristics |
Pooled total RNA isolated from mammary biopsies of 3 multiparous Holstein cows milked twice daily and biopsied at approximately day 7 of lactation.
|
| Biomaterial provider |
Anthony V. Capuco, Bovine Functional Genomics Laboratory
|
| Treatment protocol |
Three multiparous Holstein dairy cattle were milked twice daily during the first 21 days of lactation. Mammary biopsies were performed at approximately day 7 of lactation for extraction of total RNA, RNA pooling and subsequent SAGE library synthesis.
|
| Growth protocol |
Multiparous Holstein dairy cattle were evaluated during the first week of lactation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy Midi Kit (Qiagen, Valenica, CA). To remove contaminating genomic DNA, on-column DNase digestion was performed using the RNase-free DNase Set (Qiagen) according to kit instructions. RNA quality was assessed using the BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA) and concentrations were determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Rockland, DE).
|
| |
|
| Description |
This library was constructed to compare to a library constructed from pooled RNA samples obtained from mammary biopsies of dairy cows milked 4 times daily beginning at day 4 of lactation.
|
| Data processing |
SAGE2000, Version 4.5 software (Invitrogen Corp., Carlsbad, CA) was used to compare libraries, using a normalization value of 12000.
|
| |
|
| Submission date |
Oct 15, 2007 |
| Last update date |
Nov 19, 2008 |
| Contact name |
Erin E Connor |
| E-mail(s) |
erin.connor@ars.usda.gov
|
| Phone |
301-504-6104
|
| Fax |
301-504-8414
|
| Organization name |
USDA-ARS, BARC
|
| Department |
Animal and Natural Resources Institute
|
| Lab |
Bovine Functional Genomics Laboratory
|
| Street address |
10300 Baltimore Avenue
|
| City |
Beltsville |
| State/province |
MD |
| ZIP/Postal code |
20705 |
| Country |
USA |
| |
|
| Platform ID |
GPL223 |
| Series (1) |
| GSE9344 |
Gene expression in bovine mammary gland in response to increased milking frequency as determined by microarray and SAGE |
|
