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Sample GSM2356640

Query DataSets for GSM2356640

Status

Public on Jan 30, 2017

Title

72hpa_rep2

Sample type

SRA

Source name

Tadpole tail

Organism

Xenopus tropicalis

Characteristics

developmental stage: Tadpole
age: Stage 40
treatment: Tadpole tails were amputated
time: 72hours post-amputation
tissue: Tail

Extracted molecule

total RNA

Extraction protocol

Tadpole tails were amputated and immediately placed in lysis buffer (1% SDS, 0.100M NaCl, 0.010M EDTA, 0.20M Tris ph 7.6, Proteinase K) followed by ethanol precipitation to extract RNA. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Adapter sequences and low quality bases were trimmed using fastx_clipper (fastx_toolkit v 0.13.2) for single end reads and trim_galore v 0.3.3 for paired end libraries. Reads were subsequently mapped to the v9.0 genome via Tophat v2.0.13 with very-sensitive parameters.
Multimapped or unmapped reads were filtered using samtools v 1.1.
Count data was summarized via HTSeq (python v2.7). Adjustments for sequencing depth (and prior to clustering, variance stabilization through rlog transformation) were performed using DESeq2 (R v3.2.0).
Genome_build: Xentr9.0
Supplementary_files_format_and_content: Tab delimited file containing normalized count data (adjusted by size factor via DESeq2). Additional columns concerning whether a gene was called differentially expressed (DE) or if it was assigned to a fuzzy cluster are also included.

Submission date

Oct 20, 2016

Last update date

May 15, 2019

Contact name

Jessica Kay Chang

Organization name

Stanford University

Department

Genetics

Lab

Baker