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Sample GSM154135 Query DataSets for GSM154135
Status Public on Jun 22, 2007
Title Bovine Macrophage Cells Control
Sample type SAGE
Anchor NlaIII
Tag Count 78550
Tag Length 10
Source name Bovine macrophage
Organism Bos taurus
Characteristics BoMac cell line
Biomaterial provider Judith Stabel, NADC
Treatment protocol none
Growth protocol Cells were propagated in RPMI 1640 medium with 10% fetal calf serum, 100 ug/ml each streptomycin and penicillin, at 37C with 5% C02.
Extracted molecule polyA RNA
Extraction protocol Cell monolayers were disrupted with RLT+ lysis solution and total cellular RNA isolated with RNeasy kits, treated with DNaseI, followed by a second RNA isolation. PolyA RNA was enriched from total RNA using PolyATract mRNA isolation kit.
Description Standard SAGE protocols were used to generate library, cloned into pZER0-1, and sequenced on an ABI 3700 system.
Data processing Data were processed using Phred and Sequencher with manual editing then processed by eSAGE software.
Submission date Jan 05, 2007
Last update date Nov 19, 2008
Contact name Richard Zuerner
Phone 515-663-7392
Fax 515-663-7458
Organization name USDA, ARS, NADC
Department BDLRU
Lab Spirochete Diseases
Street address P.O. Box 70
City Ames
State/province IA
ZIP/Postal code 50010
Country USA
Platform ID GPL223
Series (1)
GSE6702 Changes in transcription patterns in BoMac cells in response to PDD spirochetes

Data table header descriptions
COUNT Number of Tag copies in Control library
TPM tags per million

Data table
CAAACTCTTG 682 8682.37
GGCTTTGGTC 616 7842.14
TGTGTCTGTA 584 7434.75
TTGGTGAAGG 448 5703.37
CCTCGACGAT 355 4519.41
AGCTGTGCCC 336 4277.53
TGACACGTAT 294 3742.84
TGAGAACATT 280 3564.61
AGACAGACAG 278 3539.15
CATATTTGGG 277 3526.42
GCCTGATGGG 267 3399.11
CTCACCAATA 262 3335.46
TTTGGACCCA 241 3068.11
CGTATCATTA 235 2991.73
GTGACCACGG 235 2991.73
TAGGTTGTCT 234 2978.99
CTGTTGGTGA 228 2902.61
CCCCAGCCGG 220 2800.76
GCAGAGTTCG 218 2775.30
GGTCACCAGC 215 2737.11

Total number of rows: 21951

Table truncated, full table size 410 Kbytes.

Supplementary data files not provided

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