|
Status |
Public on Apr 26, 2016 |
Title |
C2 |
Sample type |
SRA |
|
|
Source name |
RAday0 with mix1
|
Organism |
Mus musculus |
Characteristics |
cell type: Embryonic Stem Cells treatment: Day 0 - Before the addition of retinoic acid mix of spikes: mix1 ercc: mix1
|
Treatment protocol |
Four days old Ebs where treated for the next 4 days with 2uM RA (Retinoic Acid, Sigma R2625). Day of RA addition corresponds to the sample name RAday0. Four days RA tratment corresponds to the sample name RAday4.
|
Growth protocol |
Embryoid Bodies (Ebs) where generated by plating R1 mouse ES cells into 6cm low cell binding dishes as a single cell suspension (35000cells/ml) in 5ml of mES growth medium without Lif and incubating them for 4 days.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was prepared with RNeasy Mini kit (Qiagen) Mouse IVT spike-in and ERCC mixes were added to the total RNA 1microgram of total RNA was processed using the Illumina TruSeq RNA Sample Preparation Kit v2 protocol and 700ng for the Illumina TruSeq Strand Specific total RNA with RiboZero Gold protocol (Illumina). Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of 9 samples on three lanes. Between 39-59 million paired-end 100-bp reads were sequenced per sample on Illumina HiSeq Rapid 2500 instrument using protocols RTA (1.17.21.3) and HCS (2.0.12.0).
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Reads were demultiplexed the reads into the different samples Reads were aligned to the mm10 genome built and the sequences of the External RNA Control Consortium (ERCC) using Tophat (v2.0.10) RSEM (v1.2.18) was used to quantify transcripts by directly running bowtie (v2.1.0). The quantification was done on gene structures of RefSeq (mm10). Several transcripts used as spike-ins that were not present in the original gtf and were added. For the RSEM run, the transcript library was prepared (rsem-prepare-reference) followed by rsem-calculate-expression (--bowtie2 --forward-prob 0 --paired-end). Trinity’s script abundance_estimates_to_matrix.pl was used to merge the abundance estimation of the different samples and to obtain TMM normalized FPKM matrix Genome_build: mm10 Supplementary_files_format_and_content: tab-delimited text file include TMM normalized FPKM values for each sample
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|
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Submission date |
Aug 06, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Gilgi Friedlander |
Organization name |
Weizmann Institute of Science
|
Street address |
Hertzel st
|
City |
Rehovot |
ZIP/Postal code |
76100 |
Country |
Israel |
|
|
Platform ID |
GPL17021 |
Series (2) |
GSE71802 |
RNA-Seq: assessment of transcript level analysis tools [seq] |
GSE75139 |
RNA-Seq: assessment of transcript level analysis tools |
|
Relations |
SRA |
SRX1135670 |
BioSample |
SAMN03979436 |