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Sample GSM336572

Query DataSets for GSM336572

Status

Public on Dec 01, 2008

Title

young adult spe-9 hermaphrodites

Sample type

SRA

Source name

young adult spe-9

Organism

Caenorhabditis elegans

Characteristics

strain: spe-9(hc88)_hermaphrodite
developmental stage: young adult
growth condition: 20dC

Growth protocol

Wild-type N2 strains were cultured under standard conditions at 20dC and used to prepare RNAs from each developmental stage (time after staged L1; young adult (4hrs), young adult (14hrs), young adult (25hrs), young adult (36hrs) and young adult (48hrs). For library preparation from males and spermatogenesis-hermaphrodites, dpy-28;him-8 double mutants and spe-9 mutants were cultured at 23dC, respectively, and RNAs were prepraed from these two strains at 40hrs after staged L1.

Extracted molecule

total RNA

Extraction protocol

RNAs enriched for small RNA species (less than 200nt) were prepared using the mirVana miRNA Isolation kit (Ambion) with small RNA enrichment procedure. cDNA libraries for small RNAs were made from 10 µg of RNA using the DGE-Small RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina Genome Analyzer

Description

RNA enriched for small RNA species (<200nt)

Data processing

Sequences were read and raw counts reported.

Submission date

Oct 24, 2008

Last update date

May 15, 2019

Contact name

Frank J Slack

E-mail(s)

frank.slack@yale.edu

Organization name

Yale University

Department

MCDB

Street address

266 Whitney Ave

City

New Haven

State/province

ZIP/Postal code

06520

Country

USA

Platform ID

GPL9309

Series (1)

GSE13339

Changes in expression of microRNAs during C. elegans development

Relations

SRA

SRX003793

BioSample

SAMN02195658

Data table header descriptions
SEQUENCE	dots in sequences denote ambiguous base calls
COUNT	number of times sequenced

Data table
SEQUENCE	COUNT
..................................	4913
...................A.....A..A.....	1
...................A.A...AA.AA....	1
...................A.A...AAAAA....	2
...................A.AAA.AA.AA....	2
...................A.AAA.AA.AC....	1
...................A.CAC.CA.AC....	1
...................C.TCA.CA.AA....	1
.................A................	11
.................C................	13
.................G................	13
.................T................	17
................AA................	3
................AC................	1
................AG................	2
................AT................	4
................CC................	2
................CT................	2
................GA................	1
................GC................	1

Total number of rows: 2857132

Table truncated, full table size 103265 Kbytes.

Supplementary data files not provided

SRA Run Selector

Raw data are available in SRA

Processed data included within Sample table

Processed data are available on Series record