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Sample GSM958139

Query DataSets for GSM958139

Status

Public on Jan 01, 2013

Title

5g/d of yeast C3L2

Sample type

genomic

Source name

Rumen content

Organism

Characteristics

treatment: 5g/d of yeast
sample type: cow rumen content
diet: acidogenic

Treatment protocol

Whole rumen, liquid fraction (filtered through 0.2 mm) and solid fraction (recovered on the thieve after filtration) was sampled 4h after feeding for 2 days at the end of each period. Sample were frozen at -80 and freeze-dried.

Extracted molecule

genomic DNA

Extraction protocol

DNA was extracted using Qiagen Stool kit, amplified with 63F and 109R (with Bsg1 restriction site), purifed with phenol/chloroform/ethanol extraction, digested with Bsg1, concatenate, gel purified, inserted in Puc19 and clone in TOPO10.

Description

Sanger sequencing method

Data processing

Base-calling and vector sequence trimming were done using Sequence Analysis software (© Beckman Instruments, Inc.)
RSTs were separated using head-tail border 5’-ACGGGTCG-3’ or the complement 5’-CGACCCGT-3’ created by concatemerization using BioEdit = Raw data
Blast filtering to remove Chimera (95% seq ID over 90% sequence length)
Cluster sequences at 100% sequnece identity (CD-Hit-est) and count unique Tags = Processed data
Tab delimited file of the count of unique tags (100% sequence ID) after blast filtering to remove Chimera: tag sequence, count, tag ID.

Submission date

Jul 09, 2012

Last update date

Jan 01, 2013

Contact name

Eric PINLOCHE

E-mail(s)

Organization name

IBERS

Street address

Cledwyn Building

City

Aberystwyth

ZIP/Postal code

SY233DD

Country

United Kingdom

Platform ID

Series (1)

The effects of a probiotic yeast on the bacterial diversity and population structure in the rumen of cattle.

Data table header descriptions
TAG	RST sequences (5'->3')
COUNT	Frequency of each RST
RST_ID	ID of ribosomal sequence tags (RSTs)

Data table
TAG	COUNT	RST_ID
CGAACGGAGTGGTCCTCCCGAAGACCTGATTGAGCTTGCTCTTGATGGAATTCATTTGGATCACTTAGTGGCGGACGGGT	1	C3L2_10184
CGAACGAAGCGTCCCGCCCGAAGAGAAGGAGTGCTTGCACAAGTTTAATTCAATTGGGATGACTTAGTGGCGGACGGGT	1	C3L2_10191
CGGATGGAATTCATTTGAATCACTTAGTGGCGGACGGGT	3	C3L2_10217
CGAACGGAGTGGTTCTCCCGAAGACCTGAAGAGCTTGCTCAGATGGAATTCATTTGAATCACTTAGTGGCGGACGGGT	2	C3L2_10185
CGAACGGAGTGGTTCTCCCGAGGATTGACGGTGCTTGCACCAGATTGACTCATTTGAATCACTTAGTGGCGGACGGGT	1	C3L2_10169
CGAACGGAACTTTTCTCCCGACGAAATTGCGAGCTTGCTCAAGATGGAGTCATTTGAAAAGTTTAGTGGCGGACGGGT	1	C3L2_10213
CGAACGGAGTACTTCTCCCGAGACCGAGGAAGCTTGCTTCCAAAGAATCATTTGAAGTACTTAGTGGCGGACGGGT	1	C3L2_10164
CGAACGGAGTATCTCTCCCGAGACCAAAGAAGCTTGCTTCTGAGGAATCAATTGAGATACTTAGTGGCGGACGGGT	1	C3L2_10207
CGAACGGAGTTAAGCGCTGGTTTGATGCTAGCTTGCTAGTGGATTTCCTTGCTTAACTTAGTGGCGGACGGGT	2	C3L2_10158
CGAGCGGGGACATGCGACGGAGACGAAGTACTCGTACGGAGTCAAAGATGTAATGTTCTAGCGGCGGACGGGT	1	C3L2_10159
CGAACGAAGTTATCTCGCTGAGGCGAGCTTGCTCAATTCTTGAGATAACTTAGTGGCGGACGGGT	1	C3L2_10093
CGAACGGAGAATATACGCTTCAGAAGCTTCGGCAGATGATTGTATATTCTTAGTGGCGGACGGGT	1	C3L2_10147
CGAACGGAGAATTTACGCTGATGAAGCTTCGGCAGATTCTTGTAAATTCTTAGTGGCGGACGGGT	1	C3L2_10148
CGAACGGAGAATTTACGCTGATGAAGCTTCGGCAGATTCCTGTAAATTCTTAGTGGCGGACGGGT	1	C3L2_10149
CGAACGGAGATTATATAACAGAAGCCCTCGGGTGGAAGACTTATAATCTGAGGGGCGGACGGGT	1	C3L2_10130
CGAACGAAGCTCTTTTGTTGATTTTTTCGGAATGATACAAAAGATGACTTAGTGGCGGACGGGT	1	C3L2_10140
CGAACGAAGCACTTTTTTACGATCCCTTCGGGGTGACGGATTTGTGACTGAGTGGCGGACGGGT	1	C3L2_10141
CGAACGAAGCACTTTTTTACGATCCCTTCGGGGTGACGAATTTGTGACTGAGTGGCGGACGGGT	1	C3L2_10142
CGAGCGAGAATCTCTTCAGAAGCGTTTTCGGACAATTCCGAGGAGAGGAAAGCGGCGGACGGGT	1	C3L2_10143
CGAACGAAGCTTGATTTAAGATTTCTTCGGAATGATTAATGATATGACTTAGTGGCGGACGGGT	1	C3L2_10144

Total number of rows: 1266

Table truncated, full table size 14 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM958139_C3L2.txt.gz	2.3 Kb	(ftp)(http)	TXT
GSM958139_C3L2_raw.txt.gz	2.9 Kb	(ftp)(http)	TXT
Processed data included within Sample table
Processed data provided as supplementary file

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