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Sample GSM237688 Query DataSets for GSM237688
Status Public on Dec 26, 2007
Title Mammary_biopsy_IMF4_pooled (SAGE)
Sample type SAGE
Anchor NlaIII
Tag Count 7486
Tag Length 10
 
Source name biopsy of mammary parenchyma, milked 4 times daily beginning at day 4 of lactation, sampled at approx. day 7 of lactation
Organism Bos taurus
Characteristics Pooled total RNA isolated from mammary biopsies of 4 multiparous Holstein cows milked twice daily from days 1-3 of lactation and then 4 times daily beginning at day 4 of lactation. Biopsies performed at approximately day 7 of lactation.
Biomaterial provider Anthony V. Capuco, Bovine Functional Genomics Laboratory
Treatment protocol Four multiparous Holstein dairy cattle were milked twice daily during the first 3 days of lactation then 4 times daily until day 21 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 twice daily.
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

Data table header descriptions
TAG
COUNT Number of Tag copies
TPM tags per million

Data table
TAG COUNT TPM
CTGGTATAAA 1022 136521.51
AACATATCAA 574 76676.46
CACATCCGGC 441 58909.97
GCACGTCACC 362 48356.93
TTTGGAGTGG 190 25380.71
AATGGCGCTC 120 16029.92
ATACTACTGG 120 16029.92
CCTTTGAAGT 92 12289.61
GATTCCTAGT 89 11888.86
GGCAGGGCCT 87 11621.69
GTAGTTGGCT 80 10686.62
TGACACGTAT 75 10018.70
GAACAAAAAA 74 9885.12
ATGCAAGGAT 61 8148.54
TCCATTGTCA 51 6812.72
GGCTTTGGTC 49 6545.55
ACAACACATA 46 6144.80
GCCGGCCCGG 44 5877.64
ATATTTCCAA 42 5610.47
CAGAAGAGCA 42 5610.47

Total number of rows: 1352

Table truncated, full table size 26 Kbytes.




Supplementary data files not provided

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