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| Status |
Public on Jun 16, 2016 |
| Title |
P7_cre_positive_rep2 |
| Sample type |
SRA |
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| Source name |
Superior colliculus
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
development stage: P7.5
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| Treatment protocol |
Tissues were lyzed and subjected to immunoprecipitation.
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| Growth protocol |
We crossed the RiboTag knock-in mouse line (Sanz et al., Proc Natl Acad Sci U S A 106, 2009) with Pax6-alpha-Cre mouse (Marquardt et al., Cell 105, 2001).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Immunopurified RNAs are reverse-transcribed, and then amplified by a PCR-based method (Tang et al., Nat Methods 6, 2009).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Ribosome-bound mRNAs
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| Data processing |
The sequence reads were mapped to the mouse genome (mm10) using TopHat 2 version 2.0.12
Transcript assembly and estimation of FPKM (Fragments Per Kilobase of transcript per Million fragments sequenced) values were performed using Cufflinks version 2.2.1
Read counts for each gene were determined using HTSeq version 0.6.1p1. Four samples (AYRM, AYRP, ASRM and ASRP) contain read count values. The rest have FPKM.
Python script "bed2wig.py" was used to make wig files from sam files. https://github.com/daler/rdbio-scripts/blob/master/sequenceFiles/bed2wig.py
Genome_build: mm10
Supplementary_files_format_and_content: wig files, FPKM, and read counts
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| Submission date |
Mar 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christine E Holt |
| Organization name |
University of Cambridge
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| Department |
Department of PDN
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| Street address |
Anatomy Bldg., Downing St.
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| City |
Cambridge |
| ZIP/Postal code |
CB2 3DY |
| Country |
United Kingdom |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE79352 |
The dynamic translatome of retinal ganglion cell axons during assembly and maintenance of the mouse visual system |
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| Relations |
| BioSample |
SAMN04570623 |
| SRA |
SRX1650224 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2092727_P7S2.txt.gz |
80.4 Kb |
(ftp)(http) |
TXT |
| GSM2092727_P7S2.wig.gz |
5.2 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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