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Sample GSM958131

Query DataSets for GSM958131

Status

Public on Jan 01, 2013

Title

Control C1L0

Sample type

genomic

Source name

Rumen content

Organism

Characteristics

treatment: Control
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
CGAACGGAAGTCGTTATATTGATTTTGAAATGAACGGAGAACTTGTTCAAAGGGATTAGATGAAGATTTATAACAATGGCTTTAGTGGCGGACGGGT	1	C1L0_10266
CGAACGGAGTGATTCTCCCGAGGATTGACGGTGCTTGCACCTGATTGACTCATTTGAATCACTTAGTGGCGGACGGGT	1	C1L0_10243
CGAACGGAGTGGTCCTCCCGAAGACCTGAAGAGCTTGCTCGGATGGAATTCATTTGGATCACTTAGTGGCGGACGGGT	1	C1L0_10244
CGAACGGAGTGGTTCTCCCGAGGATTGACGGTGCTTGCACCTGATTGACTCATTTGAATCACTTAGTGGCGGACGGGT	1	C1L0_10245
CGAACGGGGTGATTCTCCCGAGGATTGACGGTGCTTGCACCTGATTGACTCATTTGAATCACTTAGTGGCGGACGGGT	1	C1L0_10246
CGAACCGGAGTATTCCTCCCGAGACTGAGGAAGCTTGCTTCTGAGGAATCATTTGGAATACTTAGTGGCGGACGGGT	1	C1L0_10237
CGAACGGAGAGATGATGTGAGCGGATGATTAGCTTGCTAGGATTCCAATCTTTTCATTTTCTTAGTGGCGGACGGGT	1	C1L0_10239
CGAACGGAGTATTCCTCCCGAGACCGAGGAAGCTTGCTTCTGAAGAATCACCTGGAATACTTAGTGGCGGACGGGT	1	C1L0_10233
CGAACGGAGTACTTCTCCCGAGACCGAAGAAGCTTGCTTCCAAAGAATCATTTGAAGTACTTAGTGGCGGACGGGT	1	C1L0_10236
CGAACGGAGTATTCCTCCCGAGACCGAAGAAGCTTGCTTCTGAAGAATCATTTGGAATACTTAGTGGCGGACGGGT	1	C1L0_10238
CGAGCGGGGACATGCGACGGAGACGAAGTTTTCGGATGGAGTCGAAGATGCATTGTTCTAGCGGCGGACGGGT	1	C1L0_10264
CGAGCGGGGACATACAGTGAAGAGGAAGTTTTCGGATGGAATTGGAACGGTATGTTCTAGCGGCGGACGGGT	2	C1L0_10221
CGAGCGGGGACATGCGACGGATAGGAAGTTTTCGGATGGAATTGAAGATGTATGTTCTAGCGGCGGACGGGT	1	C1L0_10222
CGAGCGGGGACATGCGACGGAGTCAAAGTTTTCGGATGGAGACGAAGATGTATGTTCTAGCGGCGGACGGGT	1	C1L0_10227
CGAGCGGAGACATACGACGGATTTGAAGTTTTCGGATGGAGATGAAGATGTATGTTTAGCGGCGGACGGGT	1	C1L0_10229
CGAACGGAGATTTAACGCTGATGAGGCTTCGGCGGATTCTTGTTAAATCTTAGTGGCGGACGGGT	2	C1L0_10211
CGAACGAAGCATTTGGAGCTGATCTCTTCGGAGTGACGCACCTTATGACTTAGTGGCGGACGGGT	2	C1L0_10212
CGAACGAAGCACTTAAGACAGATCTTTTCGGAGTGAAGACTTTTGTGACTGAGTGGCGGACGGGT	1	C1L0_10205
CGAACGGAGTGTAAACGCTGAAGCGATTTCGGTCAATTCTTGTTTATACTTAGTGGCGGACGGGT	1	C1L0_10208
CGAACGAAGCAATCAAGACAGAATCCTTCGGGAGGAAGATTTGATTGACTGAGTGGCGGACGGGT	1	C1L0_10265

Total number of rows: 172

Table truncated, full table size 11 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM958131_C1L0.txt.gz	2.3 Kb	(ftp)(http)	TXT
GSM958131_C1L0_raw.txt.gz	3.5 Kb	(ftp)(http)	TXT
Processed data included within Sample table
Processed data provided as supplementary file

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